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Aleksander SA, Anagnostopoulos AV, Antonazzo G, Arnaboldi V, Attrill H, Becerra A, Bello SM, Blodgett O, Bradford YM, Bult CJ, Cain S, Calvi BR, Carbon S, Chan J, Chen WJ, Cherry JM, Cho J, Crosby MA, De Pons JL, D’Eustachio P, Diamantakis S, Dolan ME, dos Santos G, Dyer S, Ebert D, Engel SR, Fashena D, Fisher M, Foley S, Gibson AC, Gollapally VR, Gramates LS, Grove CA, Hale P, Harris T, Hayman GT, Hu Y, James-Zorn C, Karimi K, Karra K, Kishore R, Kwitek AE, Laulederkind SJF, Lee R, Longden I, Luypaert M, Markarian N, Marygold SJ, Matthews B, McAndrews MS, Millburn G, Miyasato S, Motenko H, Moxon S, Muller HM, Mungall CJ, Muruganujan A, Mushayahama T, Nash RS, Nuin P, Paddock H, Pells T, Perrimon N, Pich C, Quinton-Tulloch M, Raciti D, Ramachandran S, Richardson JE, Gelbart SR, Ruzicka L, Schindelman G, Shaw DR, Sherlock G, Shrivatsav A, Singer A, Smith CM, Smith CL, Smith JR, Stein L, Sternberg PW, Tabone CJ, Thomas PD, Thorat K, Thota J, Tomczuk M, Trovisco V, Tutaj MA, Urbano JM, Van Auken K, Van Slyke CE, Vize PD, Wang Q, Weng S, Westerfield M, Wilming LG, Wong ED, Wright A, Yook K, Zhou P, Zorn A, Zytkovicz M. Updates to the Alliance of Genome Resources central infrastructure. Genetics 2024; 227:iyae049. [PMID: 38552170 DOI: 10.1093/genetics/iyae049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 02/28/2024] [Accepted: 02/29/2024] [Indexed: 04/09/2024] Open
Abstract
The Alliance of Genome Resources (Alliance) is an extensible coalition of knowledgebases focused on the genetics and genomics of intensively studied model organisms. The Alliance is organized as individual knowledge centers with strong connections to their research communities and a centralized software infrastructure, discussed here. Model organisms currently represented in the Alliance are budding yeast, Caenorhabditis elegans, Drosophila, zebrafish, frog, laboratory mouse, laboratory rat, and the Gene Ontology Consortium. The project is in a rapid development phase to harmonize knowledge, store it, analyze it, and present it to the community through a web portal, direct downloads, and application programming interfaces (APIs). Here, we focus on developments over the last 2 years. Specifically, we added and enhanced tools for browsing the genome (JBrowse), downloading sequences, mining complex data (AllianceMine), visualizing pathways, full-text searching of the literature (Textpresso), and sequence similarity searching (SequenceServer). We enhanced existing interactive data tables and added an interactive table of paralogs to complement our representation of orthology. To support individual model organism communities, we implemented species-specific "landing pages" and will add disease-specific portals soon; in addition, we support a common community forum implemented in Discourse software. We describe our progress toward a central persistent database to support curation, the data modeling that underpins harmonization, and progress toward a state-of-the-art literature curation system with integrated artificial intelligence and machine learning (AI/ML).
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Affiliation(s)
| | | | | | - Giulia Antonazzo
- Department of Physiology, Development and Neuroscience , University of Cambridge, Downing Street, Cambridge CB2 3DY , UK
| | - Valerio Arnaboldi
- Division of Biology and Biological Engineering 140-18, California Institute of Technology , Pasadena, CA 91125 , USA
| | - Helen Attrill
- Department of Physiology, Development and Neuroscience , University of Cambridge, Downing Street, Cambridge CB2 3DY , UK
| | - Andrés Becerra
- European Molecular Biology Laboratory, European Bioinformatics Institute , Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD , UK
| | - Susan M Bello
- The Jackson Laboratory for Mammalian Genomics, Bar Harbor , ME 04609 , USA
| | - Olin Blodgett
- The Jackson Laboratory for Mammalian Genomics, Bar Harbor , ME 04609 , USA
| | | | - Carol J Bult
- The Jackson Laboratory for Mammalian Genomics, Bar Harbor , ME 04609 , USA
| | - Scott Cain
- Informatics and Bio-computing Platform, Ontario Institute for Cancer Research , Toronto, ON M5G0A3 , Canada
| | - Brian R Calvi
- Department of Biology, Indiana University , Bloomington, IN 47408 , USA
| | - Seth Carbon
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory , Berkeley, CA
| | - Juancarlos Chan
- Division of Biology and Biological Engineering 140-18, California Institute of Technology , Pasadena, CA 91125 , USA
| | - Wen J Chen
- Division of Biology and Biological Engineering 140-18, California Institute of Technology , Pasadena, CA 91125 , USA
| | - J Michael Cherry
- Department of Genetics, Stanford University , Stanford, CA 94305
| | - Jaehyoung Cho
- Division of Biology and Biological Engineering 140-18, California Institute of Technology , Pasadena, CA 91125 , USA
| | - Madeline A Crosby
- The Biological Laboratories, Harvard University , 16 Divinity Avenue, Cambridge, MA 02138 , USA
| | - Jeffrey L De Pons
- Medical College of Wisconsin—Rat Genome Database, Departments of Physiology and Biomedical Engineering , Medical College of Wisconsin, Milwaukee, WI 53226 , USA
| | | | - Stavros Diamantakis
- European Molecular Biology Laboratory, European Bioinformatics Institute , Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD , UK
| | - Mary E Dolan
- The Jackson Laboratory for Mammalian Genomics, Bar Harbor , ME 04609 , USA
| | - Gilberto dos Santos
- The Biological Laboratories, Harvard University , 16 Divinity Avenue, Cambridge, MA 02138 , USA
| | - Sarah Dyer
- European Molecular Biology Laboratory, European Bioinformatics Institute , Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD , UK
| | - Dustin Ebert
- Department of Population and Public Health Sciences, University of Southern California , Los Angeles, CA 90033 , USA
| | - Stacia R Engel
- Department of Genetics, Stanford University , Stanford, CA 94305
| | - David Fashena
- Institute of Neuroscience, University of Oregon , Eugene, OR 97403
| | - Malcolm Fisher
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center , 3333 Burnet Ave, Cincinnati, OH 45229 , USA
| | - Saoirse Foley
- Department of Biological Sciences, Carnegie Mellon University , 5000 Forbes Ave, Pittsburgh, PA 15203
| | - Adam C Gibson
- Medical College of Wisconsin—Rat Genome Database, Departments of Physiology and Biomedical Engineering , Medical College of Wisconsin, Milwaukee, WI 53226 , USA
| | - Varun R Gollapally
- Medical College of Wisconsin—Rat Genome Database, Departments of Physiology and Biomedical Engineering , Medical College of Wisconsin, Milwaukee, WI 53226 , USA
| | - L Sian Gramates
- The Biological Laboratories, Harvard University , 16 Divinity Avenue, Cambridge, MA 02138 , USA
| | - Christian A Grove
- Division of Biology and Biological Engineering 140-18, California Institute of Technology , Pasadena, CA 91125 , USA
| | - Paul Hale
- The Jackson Laboratory for Mammalian Genomics, Bar Harbor , ME 04609 , USA
| | - Todd Harris
- Informatics and Bio-computing Platform, Ontario Institute for Cancer Research , Toronto, ON M5G0A3 , Canada
| | - G Thomas Hayman
- Medical College of Wisconsin—Rat Genome Database, Departments of Physiology and Biomedical Engineering , Medical College of Wisconsin, Milwaukee, WI 53226 , USA
| | - Yanhui Hu
- Department of Genetics, Howard Hughes Medical Institute , Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115 , USA
| | - Christina James-Zorn
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center , 3333 Burnet Ave, Cincinnati, OH 45229 , USA
| | - Kamran Karimi
- Department of Biological Sciences, University of Calgary , 507 Campus Dr NW, Calgary, AB T2N 4V8 , Canada
| | - Kalpana Karra
- Department of Genetics, Stanford University , Stanford, CA 94305
| | - Ranjana Kishore
- Division of Biology and Biological Engineering 140-18, California Institute of Technology , Pasadena, CA 91125 , USA
| | - Anne E Kwitek
- Medical College of Wisconsin—Rat Genome Database, Departments of Physiology and Biomedical Engineering , Medical College of Wisconsin, Milwaukee, WI 53226 , USA
| | - Stanley J F Laulederkind
- Medical College of Wisconsin—Rat Genome Database, Departments of Physiology and Biomedical Engineering , Medical College of Wisconsin, Milwaukee, WI 53226 , USA
| | - Raymond Lee
- Division of Biology and Biological Engineering 140-18, California Institute of Technology , Pasadena, CA 91125 , USA
| | - Ian Longden
- The Biological Laboratories, Harvard University , 16 Divinity Avenue, Cambridge, MA 02138 , USA
| | - Manuel Luypaert
- European Molecular Biology Laboratory, European Bioinformatics Institute , Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD , UK
| | - Nicholas Markarian
- Division of Biology and Biological Engineering 140-18, California Institute of Technology , Pasadena, CA 91125 , USA
| | - Steven J Marygold
- Department of Physiology, Development and Neuroscience , University of Cambridge, Downing Street, Cambridge CB2 3DY , UK
| | - Beverley Matthews
- The Biological Laboratories, Harvard University , 16 Divinity Avenue, Cambridge, MA 02138 , USA
| | - Monica S McAndrews
- The Jackson Laboratory for Mammalian Genomics, Bar Harbor , ME 04609 , USA
| | - Gillian Millburn
- Department of Physiology, Development and Neuroscience , University of Cambridge, Downing Street, Cambridge CB2 3DY , UK
| | - Stuart Miyasato
- Department of Genetics, Stanford University , Stanford, CA 94305
| | - Howie Motenko
- The Jackson Laboratory for Mammalian Genomics, Bar Harbor , ME 04609 , USA
| | - Sierra Moxon
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory , Berkeley, CA
| | - Hans-Michael Muller
- Division of Biology and Biological Engineering 140-18, California Institute of Technology , Pasadena, CA 91125 , USA
| | - Christopher J Mungall
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory , Berkeley, CA
| | - Anushya Muruganujan
- Department of Population and Public Health Sciences, University of Southern California , Los Angeles, CA 90033 , USA
| | - Tremayne Mushayahama
- Department of Population and Public Health Sciences, University of Southern California , Los Angeles, CA 90033 , USA
| | - Robert S Nash
- Department of Genetics, Stanford University , Stanford, CA 94305
| | - Paulo Nuin
- Informatics and Bio-computing Platform, Ontario Institute for Cancer Research , Toronto, ON M5G0A3 , Canada
| | - Holly Paddock
- Institute of Neuroscience, University of Oregon , Eugene, OR 97403
| | - Troy Pells
- Department of Biological Sciences, University of Calgary , 507 Campus Dr NW, Calgary, AB T2N 4V8 , Canada
| | - Norbert Perrimon
- Department of Genetics, Howard Hughes Medical Institute , Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115 , USA
| | - Christian Pich
- Institute of Neuroscience, University of Oregon , Eugene, OR 97403
| | - Mark Quinton-Tulloch
- European Molecular Biology Laboratory, European Bioinformatics Institute , Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD , UK
| | - Daniela Raciti
- Division of Biology and Biological Engineering 140-18, California Institute of Technology , Pasadena, CA 91125 , USA
| | | | | | - Susan Russo Gelbart
- The Biological Laboratories, Harvard University , 16 Divinity Avenue, Cambridge, MA 02138 , USA
| | - Leyla Ruzicka
- Institute of Neuroscience, University of Oregon , Eugene, OR 97403
| | - Gary Schindelman
- Division of Biology and Biological Engineering 140-18, California Institute of Technology , Pasadena, CA 91125 , USA
| | - David R Shaw
- The Jackson Laboratory for Mammalian Genomics, Bar Harbor , ME 04609 , USA
| | - Gavin Sherlock
- Department of Genetics, Stanford University , Stanford, CA 94305
| | - Ajay Shrivatsav
- Department of Genetics, Stanford University , Stanford, CA 94305
| | - Amy Singer
- Institute of Neuroscience, University of Oregon , Eugene, OR 97403
| | - Constance M Smith
- The Jackson Laboratory for Mammalian Genomics, Bar Harbor , ME 04609 , USA
| | - Cynthia L Smith
- The Jackson Laboratory for Mammalian Genomics, Bar Harbor , ME 04609 , USA
| | - Jennifer R Smith
- Medical College of Wisconsin—Rat Genome Database, Departments of Physiology and Biomedical Engineering , Medical College of Wisconsin, Milwaukee, WI 53226 , USA
| | - Lincoln Stein
- Informatics and Bio-computing Platform, Ontario Institute for Cancer Research , Toronto, ON M5G0A3 , Canada
| | - Paul W Sternberg
- Division of Biology and Biological Engineering 140-18, California Institute of Technology , Pasadena, CA 91125 , USA
| | - Christopher J Tabone
- The Biological Laboratories, Harvard University , 16 Divinity Avenue, Cambridge, MA 02138 , USA
| | - Paul D Thomas
- Department of Population and Public Health Sciences, University of Southern California , Los Angeles, CA 90033 , USA
| | - Ketaki Thorat
- Medical College of Wisconsin—Rat Genome Database, Departments of Physiology and Biomedical Engineering , Medical College of Wisconsin, Milwaukee, WI 53226 , USA
| | - Jyothi Thota
- Medical College of Wisconsin—Rat Genome Database, Departments of Physiology and Biomedical Engineering , Medical College of Wisconsin, Milwaukee, WI 53226 , USA
| | - Monika Tomczuk
- The Jackson Laboratory for Mammalian Genomics, Bar Harbor , ME 04609 , USA
| | - Vitor Trovisco
- Department of Physiology, Development and Neuroscience , University of Cambridge, Downing Street, Cambridge CB2 3DY , UK
| | - Marek A Tutaj
- Medical College of Wisconsin—Rat Genome Database, Departments of Physiology and Biomedical Engineering , Medical College of Wisconsin, Milwaukee, WI 53226 , USA
| | - Jose-Maria Urbano
- Department of Physiology, Development and Neuroscience , University of Cambridge, Downing Street, Cambridge CB2 3DY , UK
| | - Kimberly Van Auken
- Division of Biology and Biological Engineering 140-18, California Institute of Technology , Pasadena, CA 91125 , USA
| | - Ceri E Van Slyke
- Institute of Neuroscience, University of Oregon , Eugene, OR 97403
| | - Peter D Vize
- Department of Biological Sciences, University of Calgary , 507 Campus Dr NW, Calgary, AB T2N 4V8 , Canada
| | - Qinghua Wang
- Division of Biology and Biological Engineering 140-18, California Institute of Technology , Pasadena, CA 91125 , USA
| | - Shuai Weng
- Department of Genetics, Stanford University , Stanford, CA 94305
| | | | - Laurens G Wilming
- The Jackson Laboratory for Mammalian Genomics, Bar Harbor , ME 04609 , USA
| | - Edith D Wong
- Department of Genetics, Stanford University , Stanford, CA 94305
| | - Adam Wright
- Informatics and Bio-computing Platform, Ontario Institute for Cancer Research , Toronto, ON M5G0A3 , Canada
| | - Karen Yook
- Division of Biology and Biological Engineering 140-18, California Institute of Technology , Pasadena, CA 91125 , USA
| | - Pinglei Zhou
- The Biological Laboratories, Harvard University , 16 Divinity Avenue, Cambridge, MA 02138 , USA
| | - Aaron Zorn
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center , 3333 Burnet Ave, Cincinnati, OH 45229 , USA
| | - Mark Zytkovicz
- The Biological Laboratories, Harvard University , 16 Divinity Avenue, Cambridge, MA 02138 , USA
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Aleksander SA, Anagnostopoulos AV, Antonazzo G, Arnaboldi V, Attrill H, Becerra A, Bello SM, Blodgett O, Bradford YM, Bult CJ, Cain S, Calvi BR, Carbon S, Chan J, Chen WJ, Michael Cherry J, Cho J, Crosby MA, De Pons JL, D’Eustachio P, Diamantakis S, Dolan ME, Santos GD, Dyer S, Ebert D, Engel SR, Fashena D, Fisher M, Foley S, Gibson AC, Gollapally VR, Sian Gramates L, Grove CA, Hale P, Harris T, Thomas Hayman G, Hu Y, James-Zorn C, Karimi K, Karra K, Kishore R, Kwitek AE, Laulederkind SJF, Lee R, Longden I, Luypaert M, Markarian N, Marygold SJ, Matthews B, McAndrews MS, Millburn G, Miyasato S, Motenko H, Moxon S, Muller HM, Mungall CJ, Muruganujan A, Mushayahama T, Nash RS, Nuin P, Paddock H, Pells T, Perrimon N, Pich C, Quinton-Tulloch M, Raciti D, Ramachandran S, Richardson JE, Gelbart SR, Ruzicka L, Schindelman G, Shaw DR, Sherlock G, Shrivatsav A, Singer A, Smith CM, Smith CL, Smith JR, Stein L, Sternberg PW, Tabone CJ, Thomas PD, Thorat K, Thota J, Tomczuk M, Trovisco V, Tutaj MA, Urbano JM, Auken KV, Van Slyke CE, Vize PD, Wang Q, Weng S, Westerfield M, Wilming LG, Wong ED, Wright A, Yook K, Zhou P, Zorn A, Zytkovicz M. Updates to the Alliance of Genome Resources Central Infrastructure Alliance of Genome Resources Consortium. bioRxiv 2023:2023.11.20.567935. [PMID: 38045425 PMCID: PMC10690154 DOI: 10.1101/2023.11.20.567935] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/05/2023]
Abstract
The Alliance of Genome Resources (Alliance) is an extensible coalition of knowledgebases focused on the genetics and genomics of intensively-studied model organisms. The Alliance is organized as individual knowledge centers with strong connections to their research communities and a centralized software infrastructure, discussed here. Model organisms currently represented in the Alliance are budding yeast, C. elegans, Drosophila, zebrafish, frog, laboratory mouse, laboratory rat, and the Gene Ontology Consortium. The project is in a rapid development phase to harmonize knowledge, store it, analyze it, and present it to the community through a web portal, direct downloads, and APIs. Here we focus on developments over the last two years. Specifically, we added and enhanced tools for browsing the genome (JBrowse), downloading sequences, mining complex data (AllianceMine), visualizing pathways, full-text searching of the literature (Textpresso), and sequence similarity searching (SequenceServer). We enhanced existing interactive data tables and added an interactive table of paralogs to complement our representation of orthology. To support individual model organism communities, we implemented species-specific "landing pages" and will add disease-specific portals soon; in addition, we support a common community forum implemented in Discourse. We describe our progress towards a central persistent database to support curation, the data modeling that underpins harmonization, and progress towards a state-of-the art literature curation system with integrated Artificial Intelligence and Machine Learning (AI/ML).
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Kaldunski ML, Smith JR, Brodie KC, De Pons JL, Demos WM, Gibson AC, Hayman GT, Lamers L, Laulederkind SJF, Thorat K, Thota J, Tutaj MA, Tutaj M, Vedi M, Wang SJ, Zacher S, Dwinell MR, Kwitek AE. Rare disease research resources at the Rat Genome Database. Genetics 2023; 224:iyad078. [PMID: 37119810 PMCID: PMC10411567 DOI: 10.1093/genetics/iyad078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 04/05/2023] [Accepted: 04/19/2023] [Indexed: 05/01/2023] Open
Abstract
Rare diseases individually affect relatively few people, but as a group they impact considerable numbers of people. The Rat Genome Database (https://rgd.mcw.edu) is a knowledgebase that offers resources for rare disease research. This includes disease definitions, genes, quantitative trail loci (QTLs), genetic variants, annotations to published literature, links to external resources, and more. One important resource is identifying relevant cell lines and rat strains that serve as models for disease research. Diseases, genes, and strains have report pages with consolidated data, and links to analysis tools. Utilizing these globally accessible resources for rare disease research, potentiating discovery of mechanisms and new treatments, can point researchers toward solutions to alleviate the suffering of those afflicted with these diseases.
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Affiliation(s)
- Mary L Kaldunski
- The Rat Genome Database, Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Jennifer R Smith
- The Rat Genome Database, Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Kent C Brodie
- Clinical and Translational Science Institute, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Jeffrey L De Pons
- The Rat Genome Database, Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Wendy M Demos
- The Rat Genome Database, Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Adam C Gibson
- The Rat Genome Database, Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - G Thomas Hayman
- The Rat Genome Database, Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Logan Lamers
- The Rat Genome Database, Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Stanley J F Laulederkind
- The Rat Genome Database, Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Ketaki Thorat
- The Rat Genome Database, Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Jyothi Thota
- The Rat Genome Database, Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Marek A Tutaj
- The Rat Genome Database, Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Monika Tutaj
- The Rat Genome Database, Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Mahima Vedi
- The Rat Genome Database, Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Shur-Jen Wang
- The Rat Genome Database, Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Stacy Zacher
- Finance and Administration, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Melinda R Dwinell
- The Rat Genome Database, Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Anne E Kwitek
- The Rat Genome Database, Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
- Joint Department of Biomedical Engineering, Marquette University & Medical College of Wisconsin, Milwaukee, WI 53226, USA
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Laulederkind SJF, Hayman GT, Wang SJ, Kaldunski ML, Vedi M, Demos WM, Tutaj M, Smith JR, Lamers L, Gibson AC, Thorat K, Thota J, Tutaj MA, de Pons JL, Dwinell MR, Kwitek AE. The Rat Genome Database: Genetic, Genomic, and Phenotypic Data Across Multiple Species. Curr Protoc 2023; 3:e804. [PMID: 37347557 DOI: 10.1002/cpz1.804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/24/2023]
Abstract
The laboratory rat, Rattus norvegicus, is an important model of human health and disease, and experimental findings in the rat have relevance to human physiology and disease. The Rat Genome Database (RGD, https://rgd.mcw.edu) is a model organism database that provides access to a wide variety of curated rat data including disease associations, phenotypes, pathways, molecular functions, biological processes, cellular components, and chemical interactions for genes, quantitative trait loci, and strains. We present an overview of the database followed by specific examples that can be used to gain experience in employing RGD to explore the wealth of functional data available for the rat and other species. © 2023 Wiley Periodicals LLC. Basic Protocol 1: Navigating the Rat Genome Database (RGD) home page Basic Protocol 2: Using the RGD search functions Basic Protocol 3: Searching for quantitative trait loci Basic Protocol 4: Using the RGD genome browser (JBrowse) to find phenotypic annotations Basic Protocol 5: Using OntoMate to find gene-disease data Basic Protocol 6: Using MOET to find gene-ontology enrichment Basic Protocol 7: Using OLGA to generate gene lists for analysis Basic Protocol 8: Using the GA tool to analyze ontology annotations for genes Basic Protocol 9: Using the RGD InterViewer tool to find protein interaction data Basic Protocol 10: Using the RGD Variant Visualizer tool to find genetic variant data Basic Protocol 11: Using the RGD Disease Portals to find disease, phenotype, and other information Basic Protocol 12: Using the RGD Phenotypes & Models Portal to find qualitative and quantitative phenotype data and other rat strain-related information Basic Protocol 13: Using the RGD Pathway Portal to find disease and phenotype data via molecular pathways.
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Affiliation(s)
| | - G Thomas Hayman
- Department of Physiology, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Shur-Jen Wang
- Department of Physiology, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Mary L Kaldunski
- Department of Physiology, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Mahima Vedi
- Department of Physiology, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Wendy M Demos
- Department of Physiology, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Monika Tutaj
- Department of Physiology, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Jennifer R Smith
- Department of Physiology, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Logan Lamers
- Department of Physiology, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Adam C Gibson
- Department of Physiology, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Ketaki Thorat
- Department of Physiology, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Jyothi Thota
- Department of Physiology, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Marek A Tutaj
- Department of Physiology, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Jeffrey L de Pons
- Department of Physiology, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Melinda R Dwinell
- Department of Physiology, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Anne E Kwitek
- Department of Physiology, Medical College of Wisconsin, Milwaukee, Wisconsin
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Vedi M, Smith JR, Thomas Hayman G, Tutaj M, Brodie KC, De Pons JL, Demos WM, Gibson AC, Kaldunski ML, Lamers L, Laulederkind SJF, Thota J, Thorat K, Tutaj MA, Wang SJ, Zacher S, Dwinell MR, Kwitek AE. 2022 updates to the Rat Genome Database: a Findable, Accessible, Interoperable, and Reusable (FAIR) resource. Genetics 2023; 224:iyad042. [PMID: 36930729 PMCID: PMC10474928 DOI: 10.1093/genetics/iyad042] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Revised: 03/07/2023] [Accepted: 03/08/2023] [Indexed: 03/19/2023] Open
Abstract
The Rat Genome Database (RGD, https://rgd.mcw.edu) has evolved from simply a resource for rat genetic markers, maps, and genes, by adding multiple genomic data types and extensive disease and phenotype annotations and developing tools to effectively mine, analyze, and visualize the available data, to empower investigators in their hypothesis-driven research. Leveraging its robust and flexible infrastructure, RGD has added data for human and eight other model organisms (mouse, 13-lined ground squirrel, chinchilla, naked mole-rat, dog, pig, African green monkey/vervet, and bonobo) besides rat to enhance its translational aspect. This article presents an overview of the database with the most recent additions to RGD's genome, variant, and quantitative phenotype data. We also briefly introduce Virtual Comparative Map (VCMap), an updated tool that explores synteny between species as an improvement to RGD's suite of tools, followed by a discussion regarding the refinements to the existing PhenoMiner tool that assists researchers in finding and comparing quantitative data across rat strains. Collectively, RGD focuses on providing a continuously improving, consistent, and high-quality data resource for researchers while advancing data reproducibility and fulfilling Findable, Accessible, Interoperable, and Reusable (FAIR) data principles.
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Affiliation(s)
- Mahima Vedi
- The Rat Genome Database, Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Jennifer R Smith
- The Rat Genome Database, Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - G Thomas Hayman
- The Rat Genome Database, Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Monika Tutaj
- The Rat Genome Database, Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Kent C Brodie
- Clinical and Translational Science Institute, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Jeffrey L De Pons
- The Rat Genome Database, Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Wendy M Demos
- The Rat Genome Database, Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Adam C Gibson
- The Rat Genome Database, Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Mary L Kaldunski
- The Rat Genome Database, Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Logan Lamers
- The Rat Genome Database, Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Stanley J F Laulederkind
- The Rat Genome Database, Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Jyothi Thota
- The Rat Genome Database, Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Ketaki Thorat
- The Rat Genome Database, Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Marek A Tutaj
- The Rat Genome Database, Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Shur-Jen Wang
- The Rat Genome Database, Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Stacy Zacher
- Finance and Administration, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Melinda R Dwinell
- The Rat Genome Database, Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Anne E Kwitek
- The Rat Genome Database, Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
- Department of Biomedical Engineering, Medical College of Wisconsin, Milwaukee, WI 53226, USA
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6
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Wang SJ, Brodie KC, De Pons JL, Demos WM, Gibson AC, Hayman GT, Hill ML, Kaldunski ML, Lamers L, Laulederkind SJF, Nalabolu HS, Thota J, Thorat K, Tutaj MA, Tutaj M, Vedi M, Zacher S, Smith JR, Dwinell MR, Kwitek AE. Ontological Analysis of Coronavirus Associated Human Genes at the COVID-19 Disease Portal. Genes (Basel) 2022; 13:genes13122304. [PMID: 36553571 PMCID: PMC9777590 DOI: 10.3390/genes13122304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 12/02/2022] [Accepted: 12/04/2022] [Indexed: 12/12/2022] Open
Abstract
The COVID-19 pandemic stemmed a parallel upsurge in the scientific literature about SARS-CoV-2 infection and its health burden. The Rat Genome Database (RGD) created a COVID-19 Disease Portal to leverage information from the scientific literature. In the COVID-19 Portal, gene-disease associations are established by manual curation of PubMed literature. The portal contains data for nine ontologies related to COVID-19, an embedded enrichment analysis tool, as well as links to a toolkit. Using these information and tools, we performed analyses on the curated COVID-19 disease genes. As expected, Disease Ontology enrichment analysis showed that the COVID-19 gene set is highly enriched with coronavirus infectious disease and related diseases. However, other less related diseases were also highly enriched, such as liver and rheumatic diseases. Using the comparison heatmap tool, we found nearly 60 percent of the COVID-19 genes were associated with nervous system disease and 40 percent were associated with gastrointestinal disease. Our analysis confirms the role of the immune system in COVID-19 pathogenesis as shown by substantial enrichment of immune system related Gene Ontology terms. The information in RGD's COVID-19 disease portal can generate new hypotheses to potentiate novel therapies and prevention of acute and long-term complications of COVID-19.
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Affiliation(s)
- Shur-Jen Wang
- The Rat Genome Database, Department of Biomedical Engineering, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Kent C. Brodie
- Clinical and Translational Science Institute, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Jeffrey L. De Pons
- The Rat Genome Database, Department of Biomedical Engineering, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Wendy M. Demos
- The Rat Genome Database, Department of Biomedical Engineering, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Adam C. Gibson
- The Rat Genome Database, Department of Biomedical Engineering, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - G. Thomas Hayman
- The Rat Genome Database, Department of Biomedical Engineering, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Morgan L. Hill
- The Rat Genome Database, Department of Biomedical Engineering, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Mary L. Kaldunski
- The Rat Genome Database, Department of Biomedical Engineering, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Logan Lamers
- The Rat Genome Database, Department of Biomedical Engineering, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Stanley J. F. Laulederkind
- The Rat Genome Database, Department of Biomedical Engineering, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Harika S. Nalabolu
- The Rat Genome Database, Department of Biomedical Engineering, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Jyothi Thota
- The Rat Genome Database, Department of Biomedical Engineering, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Ketaki Thorat
- The Rat Genome Database, Department of Biomedical Engineering, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Marek A. Tutaj
- The Rat Genome Database, Department of Biomedical Engineering, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Monika Tutaj
- The Rat Genome Database, Department of Biomedical Engineering, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Mahima Vedi
- The Rat Genome Database, Department of Biomedical Engineering, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Stacy Zacher
- Finance and Administration, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Jennifer R. Smith
- The Rat Genome Database, Department of Biomedical Engineering, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Melinda R. Dwinell
- The Rat Genome Database, Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Anne E. Kwitek
- The Rat Genome Database, Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
- Correspondence:
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7
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Agapite J, Albou LP, Aleksander SA, Alexander M, Anagnostopoulos AV, Antonazzo G, Argasinska J, Arnaboldi V, Attrill H, Becerra A, Bello SM, Blake JA, Blodgett O, Bradford YM, Bult CJ, Cain S, Calvi BR, Carbon S, Chan J, Chen WJ, Michael Cherry J, Cho J, Christie KR, Crosby MA, Davis P, da Veiga Beltrame E, De Pons JL, D’Eustachio P, Diamantakis S, Dolan ME, dos Santos G, Douglass E, Dunn B, Eagle A, Ebert D, Engel SR, Fashena D, Foley S, Frazer K, Gao S, Gibson AC, Gondwe F, Goodman J, Sian Gramates L, Grove CA, Hale P, Harris T, Thomas Hayman G, Hill DP, Howe DG, Howe KL, Hu Y, Jha S, Kadin JA, Kaufman TC, Kalita P, Karra K, Kishore R, Kwitek AE, Laulederkind SJF, Lee R, Longden I, Luypaert M, MacPherson KA, Martin R, Marygold SJ, Matthews B, McAndrews MS, Millburn G, Miyasato S, Motenko H, Moxon S, Muller HM, Mungall CJ, Muruganujan A, Mushayahama T, Nalabolu HS, Nash RS, Ng P, Nuin P, Paddock H, Paulini M, Perrimon N, Pich C, Quinton-Tulloch M, Raciti D, Ramachandran S, Richardson JE, Gelbart SR, Ruzicka L, Schaper K, Schindelman G, Shimoyama M, Simison M, Shaw DR, Shrivatsav A, Singer A, Skrzypek M, Smith CM, Smith CL, Smith JR, Stein L, Sternberg PW, Tabone CJ, Thomas PD, Thorat K, Thota J, Toro S, Tomczuk M, Trovisco V, Tutaj MA, Tutaj M, Urbano JM, Van Auken K, Van Slyke CE, Wang Q, Wang SJ, Weng S, Westerfield M, Williams G, Wilming LG, Wong ED, Wright A, Yook K, Zarowiecki M, Zhou P, Zytkovicz M. Harmonizing model organism data in the Alliance of Genome Resources. Genetics 2022; 220:iyac022. [PMID: 35380658 PMCID: PMC8982023 DOI: 10.1093/genetics/iyac022] [Citation(s) in RCA: 46] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Accepted: 01/26/2022] [Indexed: 02/06/2023] Open
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.
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8
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Vedi M, Nalabolu HS, Lin CW, Hoffman MJ, Smith JR, Brodie K, De Pons JL, Demos WM, Gibson AC, Hayman GT, Hill ML, Kaldunski ML, Lamers L, Laulederkind SJF, Thorat K, Thota J, Tutaj M, Tutaj MA, Wang SJ, Zacher S, Dwinell MR, Kwitek AE. MOET: a web-based gene set enrichment tool at the Rat Genome Database for multiontology and multispecies analyses. Genetics 2022; 220:6516514. [PMID: 35380657 PMCID: PMC8982048 DOI: 10.1093/genetics/iyac005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Accepted: 01/03/2022] [Indexed: 12/12/2022] Open
Abstract
Biological interpretation of a large amount of gene or protein data is complex. Ontology analysis tools are imperative in finding functional similarities through overrepresentation or enrichment of terms associated with the input gene or protein lists. However, most tools are limited by their ability to do ontology-specific and species-limited analyses. Furthermore, some enrichment tools are not updated frequently with recent information from databases, thus giving users inaccurate, outdated or uninformative data. Here, we present MOET or the Multi-Ontology Enrichment Tool (v.1 released in April 2019 and v.2 released in May 2021), an ontology analysis tool leveraging data that the Rat Genome Database (RGD) integrated from in-house expert curation and external databases including the National Center for Biotechnology Information (NCBI), Mouse Genome Informatics (MGI), The Kyoto Encyclopedia of Genes and Genomes (KEGG), The Gene Ontology Resource, UniProt-GOA, and others. Given a gene or protein list, MOET analysis identifies significantly overrepresented ontology terms using a hypergeometric test and provides nominal and Bonferroni corrected P-values and odds ratios for the overrepresented terms. The results are shown as a downloadable list of terms with and without Bonferroni correction, and a graph of the P-values and number of annotated genes for each term in the list. MOET can be accessed freely from https://rgd.mcw.edu/rgdweb/enrichment/start.html.
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Affiliation(s)
- Mahima Vedi
- Department of Biomedical Engineering, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Harika S Nalabolu
- Department of Biomedical Engineering, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Chien-Wei Lin
- Division of Biostatistics, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Matthew J Hoffman
- Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Jennifer R Smith
- Department of Biomedical Engineering, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Kent Brodie
- Clinical and Translational Science Institute, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Jeffrey L De Pons
- Department of Biomedical Engineering, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Wendy M Demos
- Department of Biomedical Engineering, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Adam C Gibson
- Department of Biomedical Engineering, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - G Thomas Hayman
- Department of Biomedical Engineering, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Morgan L Hill
- Department of Biomedical Engineering, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Mary L Kaldunski
- Department of Biomedical Engineering, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Logan Lamers
- Department of Biomedical Engineering, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | | | - Ketaki Thorat
- Department of Biomedical Engineering, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Jyothi Thota
- Department of Biomedical Engineering, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Monika Tutaj
- Department of Biomedical Engineering, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Marek A Tutaj
- Department of Biomedical Engineering, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Shur-Jen Wang
- Department of Biomedical Engineering, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Stacy Zacher
- Information Services, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Melinda R Dwinell
- Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Anne E Kwitek
- Department of Biomedical Engineering, Medical College of Wisconsin, Milwaukee, WI 53226, USA
- Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
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9
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Kaldunski ML, Smith JR, Hayman GT, Brodie K, De Pons JL, Demos WM, Gibson AC, Hill ML, Hoffman MJ, Lamers L, Laulederkind SJF, Nalabolu HS, Thorat K, Thota J, Tutaj M, Tutaj MA, Vedi M, Wang SJ, Zacher S, Dwinell MR, Kwitek AE. The Rat Genome Database (RGD) facilitates genomic and phenotypic data integration across multiple species for biomedical research. Mamm Genome 2021; 33:66-80. [PMID: 34741192 PMCID: PMC8570235 DOI: 10.1007/s00335-021-09932-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 10/21/2021] [Indexed: 01/21/2023]
Abstract
Model organism research is essential for discovering the mechanisms of human diseases by defining biologically meaningful gene to disease relationships. The Rat Genome Database (RGD, ( https://rgd.mcw.edu )) is a cross-species knowledgebase and the premier online resource for rat genetic and physiologic data. This rich resource is enhanced by the inclusion and integration of comparative data for human and mouse, as well as other human disease models including chinchilla, dog, bonobo, pig, 13-lined ground squirrel, green monkey, and naked mole-rat. Functional information has been added to records via the assignment of annotations based on sequence similarity to human, rat, and mouse genes. RGD has also imported well-supported cross-species data from external resources. To enable use of these data, RGD has developed a robust infrastructure of standardized ontologies, data formats, and disease- and species-centric portals, complemented with a suite of innovative tools for discovery and analysis. Using examples of single-gene and polygenic human diseases, we illustrate how data from multiple species can help to identify or confirm a gene as involved in a disease and to identify model organisms that can be studied to understand the pathophysiology of a gene or pathway. The ultimate aim of this report is to demonstrate the utility of RGD not only as the core resource for the rat research community but also as a source of bioinformatic tools to support a wider audience, empowering the search for appropriate models for human afflictions.
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Affiliation(s)
- M L Kaldunski
- Department of Biomedical Engineering, The Rat Genome Database, Medical College of Wisconsin, Milwaukee, WI, USA
| | - J R Smith
- Department of Biomedical Engineering, The Rat Genome Database, Medical College of Wisconsin, Milwaukee, WI, USA
| | - G T Hayman
- Department of Biomedical Engineering, The Rat Genome Database, Medical College of Wisconsin, Milwaukee, WI, USA
| | - K Brodie
- Clinical and Translational Science Institute, Medical College of Wisconsin, Milwaukee, WI, USA
| | - J L De Pons
- Department of Biomedical Engineering, The Rat Genome Database, Medical College of Wisconsin, Milwaukee, WI, USA
| | - W M Demos
- Department of Biomedical Engineering, The Rat Genome Database, Medical College of Wisconsin, Milwaukee, WI, USA
| | - A C Gibson
- Department of Biomedical Engineering, The Rat Genome Database, Medical College of Wisconsin, Milwaukee, WI, USA
| | - M L Hill
- Department of Biomedical Engineering, The Rat Genome Database, Medical College of Wisconsin, Milwaukee, WI, USA
| | - M J Hoffman
- Department of Biomedical Engineering, The Rat Genome Database, Medical College of Wisconsin, Milwaukee, WI, USA
- Department of Physiology, Medical College of Wisconsin, Milwaukee, WI, USA
| | - L Lamers
- Department of Biomedical Engineering, The Rat Genome Database, Medical College of Wisconsin, Milwaukee, WI, USA
| | - S J F Laulederkind
- Department of Biomedical Engineering, The Rat Genome Database, Medical College of Wisconsin, Milwaukee, WI, USA
| | - H S Nalabolu
- Department of Biomedical Engineering, The Rat Genome Database, Medical College of Wisconsin, Milwaukee, WI, USA
| | - K Thorat
- Department of Biomedical Engineering, The Rat Genome Database, Medical College of Wisconsin, Milwaukee, WI, USA
| | - J Thota
- Department of Biomedical Engineering, The Rat Genome Database, Medical College of Wisconsin, Milwaukee, WI, USA
| | - M Tutaj
- Department of Biomedical Engineering, The Rat Genome Database, Medical College of Wisconsin, Milwaukee, WI, USA
| | - M A Tutaj
- Department of Biomedical Engineering, The Rat Genome Database, Medical College of Wisconsin, Milwaukee, WI, USA
| | - M Vedi
- Department of Biomedical Engineering, The Rat Genome Database, Medical College of Wisconsin, Milwaukee, WI, USA
| | - S J Wang
- Department of Biomedical Engineering, The Rat Genome Database, Medical College of Wisconsin, Milwaukee, WI, USA
| | - S Zacher
- Information Services, Medical College of Wisconsin, Milwaukee, WI, USA
| | - M R Dwinell
- Department of Biomedical Engineering, The Rat Genome Database, Medical College of Wisconsin, Milwaukee, WI, USA
- Department of Physiology, Medical College of Wisconsin, Milwaukee, WI, USA
| | - A E Kwitek
- Department of Biomedical Engineering, The Rat Genome Database, Medical College of Wisconsin, Milwaukee, WI, USA.
- Department of Physiology, Medical College of Wisconsin, Milwaukee, WI, USA.
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10
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Heywood I, Camilo F, Cotton WD, Yusef-Zadeh F, Abbott TD, Adam RM, Aldera MA, Bauermeister EF, Booth RS, Botha AG, Botha DH, Brederode LRS, Brits ZB, Buchner SJ, Burger JP, Chalmers JM, Cheetham T, de Villiers D, Dikgale-Mahlakoana MA, du Toit LJ, Esterhuyse SWP, Fanaroff BL, Foley AR, Fourie DJ, Gamatham RRG, Goedhart S, Gounden S, Hlakola MJ, Hoek CJ, Hokwana A, Horn DM, Horrell JMG, Hugo B, Isaacson AR, Jonas JL, Jordaan JDBL, Joubert AF, Józsa GIG, Julie RPM, Kapp FB, Kenyon JS, Kotzé PPA, Kriel H, Kusel TW, Lehmensiek R, Liebenberg D, Loots A, Lord RT, Lunsky BM, Macfarlane PS, Magnus LG, Magozore CM, Mahgoub O, Main JPL, Malan JA, Malgas RD, Manley JR, Maree MDJ, Merry B, Millenaar R, Mnyandu N, Moeng IPT, Monama TE, Mphego MC, New WS, Ngcebetsha B, Oozeer N, Otto AJ, Passmoor SS, Patel AA, Peens-Hough A, Perkins SJ, Ratcliffe SM, Renil R, Rust A, Salie S, Schwardt LC, Serylak M, Siebrits R, Sirothia SK, Smirnov OM, Sofeya L, Swart PS, Tasse C, Taylor DT, Theron IP, Thorat K, Tiplady AJ, Tshongweni S, van Balla TJ, van der Byl A, van der Merwe C, van Dyk CL, Van Rooyen R, Van Tonder V, Van Wyk R, Wallace BH, Welz MG, Williams LP. Inflation of 430-parsec bipolar radio bubbles in the Galactic Centre by an energetic event. Nature 2019; 573:235-237. [PMID: 31511683 DOI: 10.1038/s41586-019-1532-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Accepted: 06/28/2019] [Indexed: 11/09/2022]
Abstract
The Galactic Centre contains a supermassive black hole with a mass of four million Suns1 within an environment that differs markedly from that of the Galactic disk. Although the black hole is essentially quiescent in the broader context of active galactic nuclei, X-ray observations have provided evidence for energetic outbursts from its surroundings2. Also, although the levels of star formation in the Galactic Centre have been approximately constant over the past few hundred million years, there is evidence of increased short-duration bursts3, strongly influenced by the interaction of the black hole with the enhanced gas density present within the ring-like central molecular zone4 at Galactic longitude |l| < 0.7 degrees and latitude |b| < 0.2 degrees. The inner 200-parsec region is characterized by large amounts of warm molecular gas5, a high cosmic-ray ionization rate6, unusual gas chemistry, enhanced synchrotron emission7,8, and a multitude of radio-emitting magnetized filaments9, the origin of which has not been established. Here we report radio imaging that reveals a bipolar bubble structure, with an overall span of 1 degree by 3 degrees (140 parsecs × 430 parsecs), extending above and below the Galactic plane and apparently associated with the Galactic Centre. The structure is edge-brightened and bounded, with symmetry implying creation by an energetic event in the Galactic Centre. We estimate the age of the bubbles to be a few million years, with a total energy of 7 × 1052 ergs. We postulate that the progenitor event was a major contributor to the increased cosmic-ray density in the Galactic Centre, and is in turn the principal source of the relativistic particles required to power the synchrotron emission of the radio filaments within and in the vicinity of the bubble cavities.
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Affiliation(s)
- I Heywood
- Department of Physics, University of Oxford, Oxford, UK. .,Department of Physics and Electronics, Rhodes University, Grahamstown, South Africa. .,South African Radio Astronomy Observatory, Cape Town, South Africa.
| | - F Camilo
- South African Radio Astronomy Observatory, Cape Town, South Africa.
| | - W D Cotton
- South African Radio Astronomy Observatory, Cape Town, South Africa.,National Radio Astronomy Observatory, Charlottesville, VA, USA
| | - F Yusef-Zadeh
- CIERA and Department of Physics and Astronomy, Northwestern University, Evanston, IL, USA
| | - T D Abbott
- South African Radio Astronomy Observatory, Cape Town, South Africa
| | - R M Adam
- South African Radio Astronomy Observatory, Cape Town, South Africa
| | - M A Aldera
- Tellumat (Pty) Ltd, Retreat, South Africa
| | - E F Bauermeister
- South African Radio Astronomy Observatory, Cape Town, South Africa
| | - R S Booth
- Chalmers University of Technology, Gothenburg, Sweden
| | - A G Botha
- South African Radio Astronomy Observatory, Cape Town, South Africa
| | - D H Botha
- EMSS Antennas (Pty) Ltd, Stellenbosch, South Africa
| | - L R S Brederode
- South African Radio Astronomy Observatory, Cape Town, South Africa.,SKA Organisation, Jodrell Bank, Macclesfield, UK
| | - Z B Brits
- South African Radio Astronomy Observatory, Cape Town, South Africa
| | - S J Buchner
- South African Radio Astronomy Observatory, Cape Town, South Africa
| | - J P Burger
- South African Radio Astronomy Observatory, Cape Town, South Africa
| | - J M Chalmers
- South African Radio Astronomy Observatory, Cape Town, South Africa
| | - T Cheetham
- South African Radio Astronomy Observatory, Cape Town, South Africa
| | - D de Villiers
- Department of Electrical and Electronic Engineering, Stellenbosch University, Stellenbosch, South Africa
| | | | - L J du Toit
- EMSS Antennas (Pty) Ltd, Stellenbosch, South Africa
| | - S W P Esterhuyse
- South African Radio Astronomy Observatory, Cape Town, South Africa
| | - B L Fanaroff
- South African Radio Astronomy Observatory, Cape Town, South Africa
| | - A R Foley
- South African Radio Astronomy Observatory, Cape Town, South Africa
| | - D J Fourie
- South African Radio Astronomy Observatory, Cape Town, South Africa
| | - R R G Gamatham
- South African Radio Astronomy Observatory, Cape Town, South Africa
| | - S Goedhart
- South African Radio Astronomy Observatory, Cape Town, South Africa
| | - S Gounden
- South African Radio Astronomy Observatory, Cape Town, South Africa
| | - M J Hlakola
- South African Radio Astronomy Observatory, Cape Town, South Africa
| | - C J Hoek
- South African Radio Astronomy Observatory, Cape Town, South Africa
| | - A Hokwana
- South African Radio Astronomy Observatory, Cape Town, South Africa
| | - D M Horn
- South African Radio Astronomy Observatory, Cape Town, South Africa
| | - J M G Horrell
- IDIA, University of Cape Town, Rondebosch, South Africa
| | - B Hugo
- Department of Physics and Electronics, Rhodes University, Grahamstown, South Africa.,South African Radio Astronomy Observatory, Cape Town, South Africa
| | - A R Isaacson
- South African Radio Astronomy Observatory, Cape Town, South Africa
| | - J L Jonas
- Department of Physics and Electronics, Rhodes University, Grahamstown, South Africa.,South African Radio Astronomy Observatory, Cape Town, South Africa
| | - J D B L Jordaan
- South African Radio Astronomy Observatory, Cape Town, South Africa.,EMSS Antennas (Pty) Ltd, Stellenbosch, South Africa
| | - A F Joubert
- South African Radio Astronomy Observatory, Cape Town, South Africa
| | - G I G Józsa
- Department of Physics and Electronics, Rhodes University, Grahamstown, South Africa.,South African Radio Astronomy Observatory, Cape Town, South Africa
| | - R P M Julie
- South African Radio Astronomy Observatory, Cape Town, South Africa
| | - F B Kapp
- South African Radio Astronomy Observatory, Cape Town, South Africa
| | - J S Kenyon
- Department of Physics and Electronics, Rhodes University, Grahamstown, South Africa
| | - P P A Kotzé
- South African Radio Astronomy Observatory, Cape Town, South Africa
| | - H Kriel
- South African Radio Astronomy Observatory, Cape Town, South Africa
| | - T W Kusel
- South African Radio Astronomy Observatory, Cape Town, South Africa
| | - R Lehmensiek
- EMSS Antennas (Pty) Ltd, Stellenbosch, South Africa.,Department of Electrical Engineering, Cape Peninsula University of Technology, Bellville, South Africa
| | - D Liebenberg
- South African Radio Astronomy Observatory, Cape Town, South Africa
| | - A Loots
- Presidential Infrastructure Coordinating Commission, Pretoria, South Africa
| | - R T Lord
- South African Radio Astronomy Observatory, Cape Town, South Africa
| | - B M Lunsky
- South African Radio Astronomy Observatory, Cape Town, South Africa
| | - P S Macfarlane
- South African Radio Astronomy Observatory, Cape Town, South Africa
| | - L G Magnus
- South African Radio Astronomy Observatory, Cape Town, South Africa
| | - C M Magozore
- South African Radio Astronomy Observatory, Cape Town, South Africa
| | - O Mahgoub
- South African Radio Astronomy Observatory, Cape Town, South Africa
| | - J P L Main
- South African Radio Astronomy Observatory, Cape Town, South Africa
| | - J A Malan
- South African Radio Astronomy Observatory, Cape Town, South Africa
| | - R D Malgas
- South African Radio Astronomy Observatory, Cape Town, South Africa
| | - J R Manley
- South African Radio Astronomy Observatory, Cape Town, South Africa
| | - M D J Maree
- South African Radio Astronomy Observatory, Cape Town, South Africa
| | - B Merry
- South African Radio Astronomy Observatory, Cape Town, South Africa
| | - R Millenaar
- South African Radio Astronomy Observatory, Cape Town, South Africa
| | - N Mnyandu
- South African Radio Astronomy Observatory, Cape Town, South Africa
| | - I P T Moeng
- South African Radio Astronomy Observatory, Cape Town, South Africa
| | - T E Monama
- South African Radio Astronomy Observatory, Cape Town, South Africa
| | - M C Mphego
- South African Radio Astronomy Observatory, Cape Town, South Africa
| | - W S New
- South African Radio Astronomy Observatory, Cape Town, South Africa
| | - B Ngcebetsha
- Department of Physics and Electronics, Rhodes University, Grahamstown, South Africa.,South African Radio Astronomy Observatory, Cape Town, South Africa
| | - N Oozeer
- South African Radio Astronomy Observatory, Cape Town, South Africa.,African Institute for Mathematical Sciences, Muizenberg, South Africa
| | - A J Otto
- South African Radio Astronomy Observatory, Cape Town, South Africa
| | - S S Passmoor
- South African Radio Astronomy Observatory, Cape Town, South Africa
| | - A A Patel
- South African Radio Astronomy Observatory, Cape Town, South Africa
| | - A Peens-Hough
- South African Radio Astronomy Observatory, Cape Town, South Africa
| | - S J Perkins
- South African Radio Astronomy Observatory, Cape Town, South Africa
| | - S M Ratcliffe
- South African Radio Astronomy Observatory, Cape Town, South Africa
| | - R Renil
- South African Radio Astronomy Observatory, Cape Town, South Africa
| | - A Rust
- South African Radio Astronomy Observatory, Cape Town, South Africa
| | - S Salie
- South African Radio Astronomy Observatory, Cape Town, South Africa
| | - L C Schwardt
- South African Radio Astronomy Observatory, Cape Town, South Africa
| | - M Serylak
- South African Radio Astronomy Observatory, Cape Town, South Africa.,Department of Physics and Astronomy, University of the Western Cape, Bellville, South Africa
| | - R Siebrits
- South African Radio Astronomy Observatory, Cape Town, South Africa
| | - S K Sirothia
- Department of Physics and Electronics, Rhodes University, Grahamstown, South Africa.,South African Radio Astronomy Observatory, Cape Town, South Africa
| | - O M Smirnov
- Department of Physics and Electronics, Rhodes University, Grahamstown, South Africa.,South African Radio Astronomy Observatory, Cape Town, South Africa
| | - L Sofeya
- South African Radio Astronomy Observatory, Cape Town, South Africa
| | - P S Swart
- South African Radio Astronomy Observatory, Cape Town, South Africa
| | - C Tasse
- Department of Physics and Electronics, Rhodes University, Grahamstown, South Africa.,GEPI, CNRS, PSL Research University, Meudon, France
| | - D T Taylor
- South African Radio Astronomy Observatory, Cape Town, South Africa
| | - I P Theron
- Department of Physics and Electronics, Rhodes University, Grahamstown, South Africa.,EMSS Antennas (Pty) Ltd, Stellenbosch, South Africa
| | - K Thorat
- Department of Physics and Electronics, Rhodes University, Grahamstown, South Africa.,South African Radio Astronomy Observatory, Cape Town, South Africa
| | - A J Tiplady
- South African Radio Astronomy Observatory, Cape Town, South Africa
| | - S Tshongweni
- South African Radio Astronomy Observatory, Cape Town, South Africa
| | - T J van Balla
- South African Radio Astronomy Observatory, Cape Town, South Africa
| | - A van der Byl
- South African Radio Astronomy Observatory, Cape Town, South Africa
| | - C van der Merwe
- South African Radio Astronomy Observatory, Cape Town, South Africa
| | - C L van Dyk
- Peralex Electronics (Pty) Ltd, Bergvliet, South Africa
| | - R Van Rooyen
- South African Radio Astronomy Observatory, Cape Town, South Africa
| | - V Van Tonder
- South African Radio Astronomy Observatory, Cape Town, South Africa
| | - R Van Wyk
- South African Radio Astronomy Observatory, Cape Town, South Africa
| | - B H Wallace
- South African Radio Astronomy Observatory, Cape Town, South Africa
| | - M G Welz
- South African Radio Astronomy Observatory, Cape Town, South Africa
| | - L P Williams
- South African Radio Astronomy Observatory, Cape Town, South Africa
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