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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 isto make plant -omics data FAIR, and the first part of this work has involved thedevelopment of standards for the annotation of data sets, and their exemplary applicationto diverse data from diverse species. Finally, the annotated data has been made availablein the public repositories. In developing these standards, we have built from previous work in the field, most notablythe development of the Minimal Information about a Plant Phenotyping experiment(MIAPPE) standard (http://www.miappe.org). We have taken MIAPPE as our startingpoint, 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 activelyparticipated in the wider community developing MIAPPE, with the goal of incorporatingour 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 samematerial; moreover, what is often of interest is to connect experimental data to thephysical material assayed (or at least, related physical material, such as a stock held in agermplasm repository). We have taken special care in aligning the MIAPPE standardswith the FAO Multi Crop Passport Descriptor Data standard used by the gene banks andused the BioSamples database (http://www.ebi.ac.uk/biosamples) as an integrative layerto allow us to capture the relationships between samples and the measurements thathave been made upon them.

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. This work was presented as Deliverable D7.1 of the ELIXIR-EXCELERATE project.ELIXIR-EXCELERATE is funded by the European Commission within the Research Infrastructures programme of Horizon 2020, grant agreement number 676559.

Trabajo presentado en la Plant and Animal Genome XXII Conference, celebrada en San Diego del 11 al 15 de enero de 2014., A major breakthrough in grapevine genomics was achieved in 2007 with the sequencing of the Vitis vinifera cv. PN40024 genome. Subsequently, invaluable data related to the structural and functional characterization of the genes accumulated exponentially. Unfortunately, part of this data is episodic by nature or was acquired prior to the genome release. Furthermore, because of heterogeneous sources these data were greatly under-exploited with issues like incompatibility of data but also decentralized storage making retrieval more difficult. Classically, a large amount of useful data describing gene functions only appears in printed articles that describe the experiments carried out to answer the initial question of the publishing research team without being deposited in a common database, then remaining inaccessible for automatic data mining. High throughput “omics” data are typically stored in public repositories, but generally remain confined to their initial aim. With the objective of providing a high quality and highly accessible annotation of the grapevine genes, the International Grapevine Genome Project (IGGP) commissioned an international Supernomenclature Committee for Grape Gene Annotation to coordinate the expert-annotation effort of the grapevine genes. The goal of the committee is to provide a standard nomenclature for locus identifiers and to define the convention for the gene naming system. This system will be implemented on a new version of grapevine annotation that is being developed on an improved version of the grapevine genome chromosome assembly., Acknowledgements: GRCN NSF program, Grant Plant-KBBE-2008-GrapeReSeq, EU COST FA 1106.

Póster presentado en la 2nd Annual ConferenceFleshy Fruit Development & Ripening (COST Action FA1106 QualityFruit), celebrada en Chania (Grecia) del 22 al 25 de septiembre de 2013., A major breakthrough in grapevine genomics was achi eved in 2007 with the sequencing of the Vitis vinifera cv. PN40024 genome. Subsequently, invaluable data relat ed to the structural and functional characterization of the g enes accumulated exponentially. Unfortunately, data that were acquired prior to the genome release are largely under- exploited. Furthermore, because of heterogeneous so urces these data remain often incompatible but also decentralized storage is maki ng retrieval more difficult. Classically, a large amount of useful data describing gene functio ns only appeared in printed articles describing experiments carried out to answer specif ic questions. These data remain inaccessible for automatic text mining. High throug hput “omics” data are typically stored in public repositories, but generally are confined to their initial aim. With the objective of providing a high quality and highly accessible anno tation of grapevine genes, the International Grapevine Genome Project (IGGP) commi ssioned an international Super- nomenclature Committee for Grape Gene Annotation to coordinate the expert-annotation effort of the grapevine genes. The goal of the comm ittee is to provide a standard nomenclature for locus identifiers and to define co nventions for a gene naming system. Using previous experience acquired on similar initi atives for other plant species such as Arabidopsis , rice and tomato, a versatile system was implement ed anticipating on future developments and issues. Specific emphasis has focu sed on directions for the expert annotators by: (i) providing a clearly-identified c ommon annotation platform that also enables community-based gene curation (ii) emphasiz ing a gene naming scheme reflecting the biological features of gene products, (iii) and using a genetic ontology consistent with other organisms to facilitate evolutionary comparis on of genes.