Topic outline
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Training overviewPHENET and EMPHASIS-GO communities share converging data management issues and needs. To this end, we are organising a data management training course in Paris on 04, 05 and 06 December, open to the PHENET-EMPHASIS community.Pedagogical objectivesAt the end of this course, participants will have acquired theoretical and practical knowledge of :* the management of plant phenotyping data in accordance with FAIR principles* the use of plant community (meta)data standards.They will also have standardised a dataset in MIAPPE format and identified ways of improving the management of their data.This training is organised by PHENET and EMPHASIS with support from URGI.
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Paris - 04, 05 & 06 DecemberVenue: the training will take place at the Hôtel Mercure Paris Centre Gare MontparnasseYou're invited to join us for lunch at 12:00 on 4th of December. The training will start at 1pm and finish on Friday at 4.30pm.This training is funded by Phenome-Emphasis.fr and EMPHASIS-go.Templates links:•Crop Ontology template•MIAPPE TemplateThe training datasets are available at the bottom f this page
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Cyril Pommier (INRAE)Isabelle Alic (INRAE)Farzaneh Kazemi Pour (INRAE)Peter Selby (Cornell)Sebastian Beier (FZ Juelich)Sylvain Poque (University of Helsinki)Salvatore Cuomo (University Napoli)Sven Warris (WUR)Yin Chen (EGI)OrganisersCarla PinheiroSilvana MoscatelliChristina Gacic
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Wednesday 4/12 Thursday 5/12 Friday 6/12 First hands On, bring your own data : File template Sequence data management
Bring Your Own Data!!
Hands on submission @ EBI
Sebastian Beier (FZ Juelich)Variable building in the MIAPPE template
Isabelle Alic, Farzaneh Kazemipour,
Cyril Pommier (INRAe)Break PHIS: introduction to the Phenotyping Hybrid Information System - Isabelle Alic15 ' Break & Menti Cloud infrastructure: deploy your own analysis workflow
Yin Chen (EGI)Welcome & LunchLunchLunchIntroduction & organisation Hands On, Bring Your Own Data (PHIS, File, ...)
Isabelle Alic, Farzaneh KazemipourFAIR data and metadata
Farzaneh Kazemipour, Cyril Pommier (INRAe)Helsinki Feedback: data traceability, image and data management
Sylvain Poque (University of Helsinki)Data standards for biologists
(MIAPPE & Crop Ontology)
Cyril PommierSubmission in Dataverse & Zenodo (Canceled to save time for the other hands on)
Cyril PommierWUR ISA Based File solution (presentation + hands on)
Sven Warris (WU, NPEC)Break Break Workflows (AGENT) & DMP pragmatic
and usefull usage for RDM
Cyril PommierImages information extraction and management using AI
Salvatore Cuomo (University of Naples)Wrap up, questions, last hands on, Menti closing Data standards for computer scientists
Peter Selby (Cornell University)Feedback / discussion introduction / Menti
Carla Pinheiro (NOVA-FCT)Dinner on your own Social Diner -
FAIR data and metadata
Farzaneh Kazemipour, Cyril Pommier (INRAe)Data standards for biologists (MIAPPE & Crop Ontology)
Cyril PommierBreak Workflows (AGENT) & DMP pragmatic and usefull usage for RDM
Cyril PommierData standards for computer scientists
Peter Selby (Cornell University) -
First hands On, bring your own data : File template Variable building in the MIAPPE template
Isabelle Alic, Farzaneh Kazemipour,
Cyril Pommier (INRAe)Break PHIS: introduction to the Phenotyping Hybrid Information System - Isabelle AlicLunchHands On, Bring Your Own Data (PHIS, File, ...)
Isabelle Alic, Farzaneh KazemipourSubmission in Dataverse & Zenodo
Cyril PommierDataverse & Zenodo submission
To replace this section, attendees can access a previous recording on this subject as well as the presentation material.-
File
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Folder
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Sequence data management
Bring Your Own Data!!
Hands on submission @ EBI
Sebastian Beier (FZ Juelich)15 ' Break & Menti Cloud infrastructure: deploy your own analysis workflow
Yin Chen (EGI) -
Helsinki Feedback: data traceability, image and data management
Sylvain Poque (University of Helsinki)WUR ISA Based File solution (presentation + hands on)
Sven Warris (WU, NPEC)Helsinki Feedback: data traceability, image and data management,
See the following jupyter notebook PHIS-Data Import: 2024_PHIS-Data Import_Paris-PHENET.ipynb - Colab -
Thanks everybody!