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Tool assembly: Plant Genomics

What is the plant genomics tool assembly?

The plant genomics tool assembly is a toolkit for managing plant genomics and genotyping data throughout their life cycle, with a particular focus on ensuring traceability of the biological material to enable interoperability with plant phenotyping data. To enable this, the same persistent identifiers must be used in both the genotyping and phenotyping experiments. It is recommended that the biological plant material is accurately described using rich metadata and stored in a central repository. The tool assembly also provides guidance on how users should structure their analysis results in the form of VCF files to achieve a higher degree of interoperability.

Who can use the plant genomics tool assembly?

This tool assembly can be used by any researcher producing plant genomic or genotyping data interested in ensuring their data complies with the FAIR principles.

How can you access the plant genomics tool assembly?

All the components of this tool assembly are publicly available, but most require registration. So anyone can access the tool assembly provided they register for each tool that requires it.

For what purpose can you use the plant genomics tool assembly?

Tools and resources used in managing plant genomics and genotyping data.

Figure 1. The plant genomics tool assembly.

Metadata collection and tracking

Accurate documentation of the plant biological materials and samples is critical for interoperability, and should comply with the MIAPPE standard. This information should be submitted to BioSamples, with MIAPPE compliance validated using BioSamples’ plant-miappe.json template available on the sample validation page. Submission of sample descriptions to BioSamples can be done as early as the data collection stage, but at the latest, must acompany submission of the genomic data to the European Nucleotide Archive (ENA) or of genotyping data to the European Variation Archive (EVA). The complete timeline for submitting plant biological material to BioSamples and resulting genotyping experiment results to ENA and EVA should look like this:

  1. Register plant biological material information to BioSamples
  2. Submit Sequencing reads to ENA (using BioSamples IDs to identify material)
  3. Check if used reference genome assembly is INSDC available (GCF / GCA accesion number available)
    1. If yes proceed to submit VCF at step 4, if no proceed to step 3 b
    2. Submit reference genome assembly to INSDC (NCBI Genbank / EBML-EBI ENA / DDBJ) and wait until accession number is issued, then proceed to step 4
  4. Submit VCF file to EVA (using BioSamples IDs to identify material, GCF/GCA accession for the reference genome assembly)

e!DAL-PGP, FAIRDOM-SEEK instances such as FAIRDOMHub or Recherche Data Gouv can be used to manage and share experimental metadata, as well as data.

Data processing and analysis

Reference genomes for genome assembly and annotation should be obtained from ENSEMBL Plants or PLAZA, if available. Genetic variant data must be produced in the VCF format, and validated using the EVA vcf-validator (https://github.com/EBIvariation/vcf-validator). Please note to only use identifiers of sequences that match the reference genome assembly identifiers. In order to ensure interoperability of VCF files, the VCF meta-information lines should be used: see the Plant sciences page for more details.

Data sharing and publishing

All sequencing data collected in plant genotyping experiments should be submitted to ENA together with metadata compliant to the GSC MIxS plant associated checklist. Final results of such studies in the form of VCF files should be submitted to EVA. Additionally, supplemental data complementing these two data types is encouraged to be submitted to e!DAL-PGP or Recherche Data Gouv.

Related pages

More information

Relevant tools and resources

Skip tool table
Tool or resource Description Related pages Registry
BioSamples BioSamples stores and supplies descriptions and metadata about biological samples used in research and development by academia and industry. Plant sciences Plant Phenomics Tool info Standards/Databases Training
COPO Portal for scientists to broker more easily rich metadata alongside data to public repos. Documentation and metadata Researcher Plant sciences Machine actionability Plant Phenomics Tool info Standards/Databases
Data INRAE Dataverse for life sciences and agronomic related data Plant sciences Researcher Data Steward: research Plant Phenomics Standards/Databases
Data Stewardship Wizard Publicly available online tool for composing smart data management plans Data management plan Researcher Data Steward: research Data Steward: infrastructure NeLS TSD Plant Phenomics Tool info Training
e!DAL-PGP Plant Genomics and Phenomics Research Data Repository Plant sciences Researcher Data Steward: research Data Steward: infrastructure Data publication Documentation and metadata Plant Phenomics Standards/Databases
Ensembl Plants Open-access database of full genomes of plant species. Plant sciences Standards/Databases Training
European Nucleotide Archive (ENA) A record of sequence information scaling from raw sequcning reads to assemblies and functional annotation Microbial biotechnology Data brokering Tool info Standards/Databases Training
European Variation Archive (EVA) Open-access database of all types of genetic variation data from all species. Tool info Standards/Databases Training
FAIDARE FAIDARE is a tool allowing to search data across dinstinct databases that implemented BrAPI. Researcher Data Steward: research Plant sciences IFB Plant Phenomics Tool info
FAIRDOM-SEEK A data Management Platform for organising, sharing and publishing research datasets, models, protocols, samples, publications and other research outcomes. Data storage Data Steward: infrastructure NeLS Microbial biotechnology IFB Machine actionability Plant Phenomics Tool info Training
MIAPPE Minimum Information About a Plant Phenotyping Experiment Documentation and metadata Researcher Data Steward: research Plant sciences Plant Phenomics Standards/Databases Training
MIxS Minimum Information about any (x) Sequence Documentation and metadata Researcher Data Steward: research Marine metagenomics Standards/Databases Training
Multi-Crop Passport Descriptor (MCPD) The Multi-Crop Passport Descriptor is the metadata standard for plant genetic resources maintained ex situ by genbanks. Documentation and metadata Researcher Data Steward: infrastructure Data Steward: policy Plant sciences Plant Phenomics Standards/Databases
pISA-tree A data management solution for intra-institutional organization and structured storage of life science project-associated research data, with emphasis on the generation of adequate metadata. Microbial biotechnology Researcher Data Steward: research Data organisation Documentation and metadata Plant Phenomics Tool info
PLAZA Access point for plant comparative genomics, centralizing genomic data produced by different genome sequencing initiatives. Plant sciences Researcher Standards/Databases Training
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