Workshop on Resources for Plant Sciences, 2023

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• Select section Workshop on Resources for Plant Sciences

  Workshop on Resources for Plant Sciences

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  • Select activity Within the ELIXIR implementation study INCREASING ...

    Within the ELIXIR implementation study INCREASING we have prepared three plant tool bundles, each one a systematic organisation of tools to enable their maximum potential to users, including detailed instructions for use. These bundles are designed to make existing tools, dealing with various plant-derived data, better accessible to the end user. 

    To present all three bundles to researchers, an online workshop was organised between October 5th and 6th 2023. The workshop included three sessions covering the three bundles, and the recordings and materials of these sessions are provided here. 

    The bundles are:

• Select section 1. Plant orthology bundle

  1. Plant orthology bundle

  • Select activity The increased availability of high-throughput mult...

    The increased availability of high-throughput multi-omics methods is providing an extended resolution of different genetic and metabolic processes occurring in various plant species. Given the contrasting levels of detail in gene/protein functional annotations between model and non-model plant species, comparative approaches based on sequence similarity and homology are often applied. Comparative genomics approaches across different species are also essential to understand the evolution of specific traits.   

    Different genomic resources, often linked to whole-genome sequencing initiatives, include or are based on the prediction of homology links between genes, either orthologs or paralogs and functional annotation based on Gene Ontology or MapMan ontologies.  This bundle presents the principles, benefits and drawbacks of three different plant orthology detection tools: Ensembl Plants, Plaza, Mercator, MapMan, and GoMapMan.

    More information about the bundle is available here: PlantSciences-INCREASING - Plant Orthology Bundle 

    Workshop presentations:

    
    
    
  • Select activity PlantSciences-INCREASING-2023.10-Plant-Orthology-Bundle

    

    PlantSciences-INCREASING-2023.10-Plant-Orthology-Bundle File
  • Select activity PlantSciences-INCREASING-2023.10-Plant-Orthology-Bundle-GoMapMan

    

    PlantSciences-INCREASING-2023.10-Plant-Orthology-Bundle-GoMapMan File
  • Select activity PlantSciences-INCREASING-2023.10-Plant-Orthology-Bundle-PLAZA

    

    PlantSciences-INCREASING-2023.10-Plant-Orthology-Bundle-PLAZA File
  • Select activity https://elixir.mf.uni-lj.si/draftfile.php/6672/use...

     

     

• Select section 2. Plant data analysis & visualisation tools

  2. Plant data analysis & visualisation tools

  • Select activity This bundle is primarily intended for researchers ...

    This bundle is primarily intended for researchers who work with complex datasets generated at multiple molecular levels, such as multi-omics datasets or any other heterogeneous dataset. The bundle includes the plant specific knowledge graphs: KnetMiner, AgroLD, and Stress Knowledge Map, the federated search engine FAIDARE, and the data integration and visualisation tools DiNaR and MapMan. In the bundle we present principles and examples of the use of knowledge graphs for plant science, including how they can be interactively explored in relation to genes, proteins, or metabolites of interest. Finally, we show how they can be connected to the tools DiNaR and MapMan  to contextualise data  within prior knowledge, specifically  for visualisation of data (e.g. gene expression) on top of knowledge networks and pathway maps. 

    More information about the bundle is available here: PlantSciences-INCREASING - Plant data analysis and visualisation bundle  

    Workshop presentation:

    
    
    
  • Select activity PlantSciences-INCREASING-2023.10-Visualisation- -Data-Analysis-Bundle

    

    PlantSciences-INCREASING-2023.10-Visualisation- -Data-Analysis-Bundle File
  • Select activity PlantSciences-INCREASING-2023.10-Visualisation- -Data-Analysis-Bundle-KnetMiner

    

    PlantSciences-INCREASING-2023.10-Visualisation- -Data-Analysis-Bundle-KnetMiner File
  • Select activity Text and media area

       

       

• Select section 3. Plant Phenotyping data publication using MIAPPE, dataverse and e!DAL-PGP

  3. Plant Phenotyping data publication using MIAPPE, dataverse and e!DAL-PGP

  • Select activity In this bundle, we demonstrate phenotyping data or...

    In this bundle, we demonstrate phenotyping data organisation and description using MIAPPE for publication in generic data repositories such as dataverse or e!DAL-PGP. This was based on the guidelines published on the RDMkit and the FAIR cookbook.

    More information about the bundle is available here: PlantSciences-INCREASING - Plant data publication 

    Workshop presentations:
    

    
    
    
  • Select activity PlantSciences-INCREASING-2023.10-Phenotyping-Data-Publication-Bundle

    

    PlantSciences-INCREASING-2023.10-Phenotyping-Data-Publication-Bundle File
  • Select activity PlantSciences-INCREASING-2023.10-Phenotyping-Data-Publication-MIAPPE-OVERVIEW

    

    PlantSciences-INCREASING-2023.10-Phenotyping-Data-Publication-MIAPPE-OVERVIEW File
  • Select activity https://elixir.mf.uni-lj.si/draftfile.php/6672/use...