Toward a data infrastructure for the Plant Cell Atlas

Author:

Fahlgren Noah1ORCID,Kapoor Muskan2ORCID,Yordanova Galabina3ORCID,Papatheodorou Irene3ORCID,Waese Jamie4ORCID,Cole Benjamin5ORCID,Harrison Peter3ORCID,Ware Doreen67ORCID,Tickle Timothy8ORCID,Paten Benedict9ORCID,Burdett Tony3ORCID,Elsik Christine G10ORCID,Tuggle Christopher K2ORCID,Provart Nicholas J4ORCID

Affiliation:

1. Donald Danforth Plant Science Center , Saint Louis, Missouri 63132, USA

2. Bioinformatics and Computational Biology Program, Department of Animal Science, Iowa State University , Ames, Iowa 50011, USA

3. EMBL-EBI, Wellcome Genome Campus , Hinxton, Cambridgeshire, CB10 1SD, UK

4. Department of Cell and Systems Biology/Centre for the Analysis of Genome Evolution and Function, University of Toronto , Toronto, Ontario M5S 3B2, Canada

5. DOE-Joint Genome Institute, Lawrence Berkeley National Laboratory , 1, Cyclotron Road , Berkeley, California 94720, USA

6. Cold Spring Harbor Laboratory , One Bungtown Road, Cold Spring Harbor , New York 11724, USA

7. USDA ARS NAA Robert W. Holley Center for Agriculture and Health , Ithaca, New York 14853, USA

8. Data Sciences Platform, The Broad Institute of MIT and Harvard , 415 Main Street , Cambridge, Massachusetts 02142, USA

9. UC Santa Cruz Genomics Institute, Baskin School of Engineering , 1156 High Street , Santa Cruz, California 95064, USA

10. Division of Animal Sciences/Division of Plant Science & Technology/Institute for Data Science & Informatics, University of Missouri , Columbia, Missouri 65211, USA

Abstract

AbstractWe review how a data infrastructure for the Plant Cell Atlas might be built using existing infrastructure and platforms. The Human Cell Atlas has developed an extensive infrastructure for human and mouse single cell data, while the European Bioinformatics Institute has developed a Single Cell Expression Atlas, that currently houses several plant data sets. We discuss issues related to appropriate ontologies for describing a plant single cell experiment. We imagine how such an infrastructure will enable biologists and data scientists to glean new insights into plant biology in the coming decades, as long as such data are made accessible to the community in an open manner.

Funder

National Sciences and Engineering Research Council of Canada

NSERC

United States Department of Agriculture

Agricultural Genome to Phenome Initiative

Publisher

Oxford University Press (OUP)

Subject

Plant Science,Genetics,Physiology

Reference106 articles.

1. A science driven production cyberinfrastructure—the open science grid;Altunay;J Grid Comput,2011

2. VEuPathDB: the eukaryotic pathogen, vector and host bioinformatics resource center;Amos;Nucleic Acids Res,2022

3. Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature,2000

4. Computational principles and challenges in single-cell data integration.;Argelaguet;Nat Biotechnol

5. KBase: The United States department of energy systems biology knowledgebase;Arkin;Nat Biotechnol,2018

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