Trans-national Infrastructure for Plant Genomic Science

    Project: EU research project

    Project Details

    Description

    Food and energy security are major challenges facing humanity in the coming decades. The falling costs of nucleotide sequencing are opening up significant opportunities for crop improvement through plant breeding and increased understanding of plant biology; in particular through interpreting the growing volume of plant genomics data in the context of phenotype. However, at present, there is no adequare infrastructre for plant genomic data. transPLANT will develop a new infrastructure for this data, leveraging the experience of medical informatics while addressing the particular challenges and opportunities of plant genomics.
    Compared with vertebrate genomes, plant genomes may be large and have complex evolutinary histories, which makes their analysis a hard problem (both in terms of theory, and in terms of the compute resources required for data storage and analysis). Issues include genome size, polyploidy, and the quantity, diversity and dispersed nature of data in need of integration.
    To address these problems, transPLANT will develop distributed solutions, exploiting the expertise of the project partners in particular species and problems to provide a seamless set of computational and interactive services to the plant research community. These services will be developed on top of the outputs of RTD activities designed to build new repositories and develop new algorithms, and with the input from the plant science and other related communities garnered through extensive networking activities. A series of training workshops will educate the community in the use of transPLANT tools and data.
    transPLANT will be built on standard technologies for data exchange and representation, service provision, virtual compute infrastructure, and interface development; where such standards are currently lacking (as in phenotype description), they will be developed in the context of the project.
    AcronymtransPLANT
    StatusFinished
    Effective start/end date1/09/1131/08/15

    Research Output

    Similarities between plant traits based on their connection to underlying gene functions

    Nap, J. P., Sanchez-Perez, G. F. & van Dijk, A-J., 2017, In : PLoS ONE. 12, 8, e0182097.

    Research output: Contribution to journalArticleAcademicpeer-review

    Open Access
  • The KnownLeaf literature curation system captures knowledge about Arabidopsis leaf growth and development and facilitates integrated data mining

    Szakonyi, D., van Landeghem, S., Baerenfaller, K., Baeyens, L., Blomme, J., Casanova-Saéz, R., De Bodt, S., Esteve-Bruna, D., Fiorani, F., Gonzalez, N., Grønlund, J., Immink, R. G. H., Jover-Gil, S., Kuwabara, A., Muñoz-Nortes, T., van Dijk, A. D. J., Wilson-Sánchez, D., Buchanan-Wollaston, V., Angenent, G. C., Van de Peer, Y. & 5 others, Inzé, D., Micol, J. L., Gruissem, W., Walsh, S. & Hilson, P., 2015, In : Current Plant Biology. 2, p. 1-11

    Research output: Contribution to journalArticleAcademicpeer-review

    Open Access
  • 4 Citations (Scopus)

    Biological process annotation of proteins across the plant kingdom

    Bargsten, J. W., Severing, E. I., Nap, J. P. H., Sanchez Perez, G. F. & van Dijk, A. D. J., 2014, In : Current Plant Biology. 1, p. 73-82

    Research output: Contribution to journalArticleAcademicpeer-review

  • 6 Citations (Scopus)