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Plant genomic and genetic variation data submission to EMBL-EBI databases
Plant genomic and genetic variation data submission to EMBL-EBI databases
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Description

This recipe provides guidance for submitting plant genotyping data to public repositories. It explains in a step-wise fashion which work should be done and when. Special attention should be paid to the metadata maintenance of the data that will be deposited in different repositories as part of this recipe. A prerequisite for fully understanding this recipe is a basic knowledge of the MIAPPE standard (https://fairsharing.org/bsg-s000543/). The exact listing of the metadata fields required for a FAIRification of the genotyping data set within a VCF file is also part of this recipe with examples and explanations (See details in Section 4.2).
Details

URL: https://faircookbook.elixir-europe.org/content/recipes/reusability/miappe.htmlCommunities:Disciplines:Target Groups:
  • Researcher
Proficiency Levels:
  • Novice
  • Advanced Beginner

FAIR Cookbook - Publication of plant experimental data in generic data repositories
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FAIR Cookbook - Publication of plant experimental data in generic data repositoriesThe FAIR Cookbook is an online, open and live resource for the Life Sciences with recipes that help you to make and keep data Findable, Accessible, Interoperable and Reusable; in one word FAIR. This recipe describes best practices for submitting plant experimentation data to generic data repositories (e.g. e!DAL-PGP, Dataverses such as recherche.data.gouv, dmportal.biodata.pt and Jülich DATA). This will allow data reuse according to FAIR principles, and especially to ensure visibility and reuse of genetic and phenomic datasets via minimal and sufficient description: data type, organism, list of plant material used, experimental metadata including methods and protocols, etc. Maximizing data visibility by allowing their indexation in international portals, as well as ensuring the interoperability of data sets in relation to a coherent identification of plant material used in experiments of various kinds (phenotyping, genotyping, genomics, etc.).
Learning Resource Type
Cookbook
File Format
MD
Languages
English
Media Type
Text
License
CCBY
Authors
Keywords
#Repositories#Data Publishing#Genotyping Data#MIAPPE#Plant Phenotyping Data#FAIR Principles
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Webinar on Plant Data Management for Phenotyping Experiments
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Webinar on Plant Data Management for Phenotyping ExperimentsThe Minimal Information About Plant Phenotyping Experiment, MIAPPE (www.miappe.org) has been designed by ELIXIR, EMPHASIS and Bioversity international to guide plant scientists in the management of experimental data and to facilitate integration with genotyping data.The webinar gives an overview of the current practices and methods for plant phenotyping data standardization.
Learning Resource Type
Lecture
File Format
PDF
Languages
English
Media Type
Presentation
Publication Date
2021-04-02
License
CCBY
Size
3.1 MB
Authors
Keywords
#MIAPPE#Data Management#BrAPI#Ontologies#Phenotyping Experiments#Plant Data
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Webinar on Plant Data Management for Phenotyping Experiments
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Webinar on Plant Data Management for Phenotyping ExperimentsThe Minimal Information About Plant Phenotyping Experiment, MIAPPE (www.miappe.org) has been designed by ELIXIR, EMPHASIS and Bioversity international to guide plant scientists in the management of experimental data and to facilitate integration with genotyping data.The webinar gives an overview of the current practices and methods for plant phenotyping data standardization.
Learning Resource Type
Lecture
File Format
Unknown
Languages
English
Media Type
Video
Publication Date
2021-04-02
License
CCBY
Authors
Keywords
#MIAPPE#Data Management#BrAPI#Ontologies#Phenotyping Experiments#Plant Data
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FAIR Cookbook - Plant genomic and genetic variation data submission to EMBL-EBI databases
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FAIR Cookbook - Plant genomic and genetic variation data submission to EMBL-EBI databasesThe FAIR Cookbook is an online, open and live resource for the Life Sciences with recipes that help you to make and keep data Findable, Accessible, Interoperable and Reusable; in one word FAIR. This recipe provides guidance for submitting plant genotyping data to public repositories. It explains in a step-wise fashion which work should be done and when. Special attention should be paid to the metadata maintenance of the data that will be deposited in different repositories as part of this recipe. A prerequisite for fully understanding this recipe is a basic knowledge of the MIAPPE standard. The exact listing of the metadata fields required for a FAIRification of the genotyping data set within a VCF file is also part of this recipe with examples and explanations.
Learning Resource Type
Cookbook
File Format
MD
Languages
English
Media Type
Text
License
CCBY
Authors
Keywords
#Repositories#Data Publishing#Genotyping Data#MIAPPE#Plant Phenotyping Data#FAIR#BioSamples
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Forschungsdatenmanagement für Agrarwissenschaftler und Biologen
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Forschungsdatenmanagement für Agrarwissenschaftler und BiologenPresentation slides for a Workshop about research data management for students and researchers of agricultural sciences and biology. Workshop held at Humboldt-Universität zu Berlin, 12 May 2016.
Learning Resource Type
Lecture
File Format
PPTX, ODP, PDF
Languages
German
Media Type
Presentation
Publication Date
2016-05-27
License
CCBY
Authors
Keywords
#Repositories#Data Journals#Data Paper#Metadata#Pangaea#Research Data#Research Data Management#re3data
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RDMkit - Plant Science
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RDMkit - Plant ScienceThe RDMkit is a guide for life scientists in their efforts to better manage their research data following the FAIR Principles. It is based on the various steps of the data lifecycle, although not all the steps will be relevant to everyone. This section describes domain-specific aspects as well as Tools and Resources for plant science. It focuses on the planning of plant science data management, as well as the collection of phenotyping data and genotyping data.
Learning Resource Type
Cookbook
File Format
Unknown
Languages
English
Media Type
Text
Publication Date
2023-12-20
License
CCBY
Authors
Keywords
#Plant Phenotyping Data#Data Collection#Data Management Planning#Plant Genotyping Data
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