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AgroLD: A Knowledge Graph Database for Plant Functional Genomics

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Plant Bioinformatics

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2443))

Abstract

Recent advances in high-throughput technologies have resulted in tremendous increase in the amount of data in the agronomic domain. There is an urgent need to effectively integrate complementary information to understand the biological system in its entirety. We have developed AgroLD, a knowledge graph that exploits the Semantic Web technology and some of the relevant standard domain ontologies, to integrate information on plant species and in this way facilitating the formulation of new scientific hypotheses. This chapter outlines some integration results of the project, which initially focused on genomics, proteomics and phenomics.

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Acknowledgments

The authors thank the technical staff of the South Green Bioinformatics platform for their support. They thank the providers of databases listed in Table 2, who kindly gave access to their publicly datasets. They thank the expert biologists and bioinformaticians who contributed to the testing sessions and helped to improve the content of the system and the user interface.

Author information

Authors and Affiliations

  1. DIADE, IRD, CIRAD, Univ. Montpellier, Montpellier, France

    Pierre Larmande

  2. French Institute of Bioinformatics (IFB)—South Green Bioinformatics Platform, Bioversity, CIRAD, INRAE, IRD, Montpellier, France

    Pierre Larmande, Gildas Tagny Ngompe & Manuel Ruiz

  3. AGAP, CIRAD, INRAE, Univ. Montpellier, av Agropolis, Montpellier, France

    Gildas Tagny Ngompe & Manuel Ruiz

  4. EMBL-EBI, Wellcome Genome Campus, Cambridgeshire, UK

    Aravind Venkatesan

Authors
  1. Pierre Larmande
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  2. Gildas Tagny Ngompe
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  3. Aravind Venkatesan
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  4. Manuel Ruiz
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Corresponding author

Correspondence to Pierre Larmande .

Editor information

Editors and Affiliations

  1. School of Biological Sciences, University of Western Australia, Perth, WA, Australia

    David Edwards

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© 2022 The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature

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Larmande, P., Tagny Ngompe, G., Venkatesan, A., Ruiz, M. (2022). AgroLD: A Knowledge Graph Database for Plant Functional Genomics. In: Edwards, D. (eds) Plant Bioinformatics. Methods in Molecular Biology, vol 2443. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-2067-0_28

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  • DOI: https://doi.org/10.1007/978-1-0716-2067-0_28

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-2066-3

  • Online ISBN: 978-1-0716-2067-0

  • eBook Packages: Springer Protocols

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