Project deliverable Open Access

Datasets annotated for at least 1 woody plant, cereal and solanaceous species; genotype, phenotype and sample metadata submitted to appropriate public archives

Adam-Blondon, Anne-Françoise; Chaves, Inês; Coppens, Friederik; Costa, Bruno; Finkers, Richard; Horro, Carlos; Kersey, Paul; Mihotey, Celia; Miguel, Celia; Papoutsoglu, Evangelia; Pommier, Cyril; Ramsak, Ziva

Plant omics data is often not published, or dispersed among multiple repositories and, owing to poor annotation of submissions with descriptive metadata, effectively not FAIR (i.e. Findable, Accessible, Interoperable and Re-usable). In this work package, our goal is to make plant -omics data FAIR, and the first part of this work has involved the development of standards for the annotation of data sets, and their exemplary application to diverse data from diverse species. Finally, the annotated data has been made available in the public repositories.

In developing these standards, we have built from previous work in the field, most notably the development of the Minimal Information about a Plant Phenotyping experiment (MIAPPE) standard (http://www.miappe.org). We have taken MIAPPE as our starting point, and extended and revised it according to the characteristics of our exemplar data.

Because a proposed standard becomes a real one through its adoption, we have actively participated in the wider community developing MIAPPE, with the goal of incorporating our developments within the official MIAPPE specification. 

A particularly important issue is the identification of material used in an experiment.Materials used within and between experiments may be related to each other (by time, space, condition or genealogy), and multiple assays may be taken from the same material; moreover, what is often of interest is to connect experimental data to the physical material assayed (or at least, related physical material, such as a stock held in a germplasm repository). We have taken special care in aligning the MIAPPE standards with the FAO Multi Crop Passport Descriptor Data standard used by the gene banks and used the BioSamples database (http://www.ebi.ac.uk/biosamples) as an integrative layer to allow us to capture the relationships between samples and the measurements that have been made upon them.

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