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Updates to the Alliance of Genome Resources central infrastructure

Journal Article · · Genetics (Online)
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  1. Stanford Univ., CA (United States); The Alliance of Genome Resources Consortium. et al.
  2. The Jackson Laboratory for Mammalian Genomics, Bar Harbor , ME 04609 , USA
  3. Department of Physiology, Development and Neuroscience , University of Cambridge, Downing Street, Cambridge CB2 3DY , UK
  4. Division of Biology and Biological Engineering 140-18, California Institute of Technology , Pasadena, CA 91125 , USA
  5. European Molecular Biology Laboratory, European Bioinformatics Institute , Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD , UK
  6. Institute of Neuroscience, University of Oregon , Eugene, OR 97403
  7. Informatics and Bio-computing Platform, Ontario Institute for Cancer Research , Toronto, ON M5G0A3 , Canada
  8. Department of Biology, Indiana University , Bloomington, IN 47408 , USA
  9. Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory , Berkeley, CA
  10. Department of Genetics, Stanford University , Stanford, CA 94305
  11. The Biological Laboratories, Harvard University , 16 Divinity Avenue, Cambridge, MA 02138 , USA
  12. Medical College of Wisconsin—Rat Genome Database, Departments of Physiology and Biomedical Engineering , Medical College of Wisconsin, Milwaukee, WI 53226 , USA
  13. NYU Grossman School of Medicine, New York , NY 10016
  14. Department of Population and Public Health Sciences, University of Southern California , Los Angeles, CA 90033 , USA
  15. Division of Developmental Biology, Cincinnati Children's Hospital Medical Center , 3333 Burnet Ave, Cincinnati, OH 45229 , USA
  16. Department of Biological Sciences, Carnegie Mellon University , 5000 Forbes Ave, Pittsburgh, PA 15203
  17. Department of Genetics, Howard Hughes Medical Institute , Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115 , USA
  18. Department of Biological Sciences, University of Calgary , 507 Campus Dr NW, Calgary, AB T2N 4V8 , Canada
+ Show Author Affiliations
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).
Research Organization:
Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
Sponsoring Organization:
National Institutes of Health (NIH); USDOE; USDOE Office of Science (SC), Biological and Environmental Research (BER). Biological Systems Science (BSS)
Contributing Organization:
The Alliance of Genome Resources Consortium
Grant/Contract Number:
AC02-05CH11231
OSTI ID:
2345960
Alternate ID(s):
OSTI ID: 2477236
Journal Information:
Genetics (Online), Journal Name: Genetics (Online) Journal Issue: 1 Vol. 227; ISSN 1943-2631
Publisher:
Oxford University Press; Genetics Society of AmericaCopyright Statement
Country of Publication:
United States
Language:
English

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Related Subjects

59 BASIC BIOLOGICAL SCIENCES
97 MATHEMATICS AND COMPUTING
Caenorhabditis elegans
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zebrafish