Pilot Projects Workshop COST INTEGRAPE
22-23 January 2020
Lisbon, Portugal

GOAL: Three activities, transversal to the current working groups will start, feeding the WG deliverables based on use cases: – One working on reference gene datasets, guidelines and repositories necessary for the integration of transcriptomic, metabolomics and proteomic data – One working on data standardisation for phenotypes – One working on reference data sets, submission processes to archives of genomes. The face to face working group meeting gathers the WG leaders and the pilot projects coordinators to work on guidelines or other outputs. One of the deliverables is to have a list of recommended repositories for the community.

Dates: 22-23 January 2020

Venue: Building C2, rooms 2.2.22 e 2.2.24. Faculdade de Ciencias da Universidade de Lisboa, Campo Grande, 1749-016 Lisbon Portugal


2020 January 22nd Wednesday

9h00-9h30. Welcome
9h30-10h00. Daniel Faria (ELIXIR Portugal). Activities of the ELIXIR plant community
10h00-10h30. Björn Usadel (EMPHASIS). The plant pilot in EOSC-Life
10h30-11h00. Alessandro Cestaro (ELIXIR Italy). Apple as a Model for Genomic
Information Exchange (the Italian implementation study on apple)
11h00-11h30. Coffee break Building C6
11h30-12h00. Kristina Gruden. “Tools for Multi-OMICs integration”
12h00-12h30. Discussion on the deliverables of the COST action/ Status of the first
training school
12h30-14h00. Lunch Building C6
14h00- 16h00. Session on the “genome data” pilot by video conference with the group
of Doreen Ware – Coord. Camille Rustenholz
– Toward genome submission guidelines: pilot project ongoing (where, who,
– Toward the use of Gramene to perform comparative genomics in grapevine: the
work of Doreen’s group on an automated pipeline to get standardized gene annotations
– Feedback and discussion

16h00-16h30 Coffee break Building C6
16h30-18h00. Session on the “multi-omics” pilot – (Coord. Jérôme Grimplet)
– Presentation of the SNF project
– Workplan for using it as the pilot project for good practice on transcriptomic,
metabolomic and data integration
– Feedback from the core group and discussion
– Check the plans of the data management part of the first training school

2020 January 23rd Thursday

9h00-11h00. Session on the “Plant phenotyping” pilot – Coord. Éric Duchêne
● Advancement of the work package on the controlled vocabulary for the organs and for the phenotyping variables

● How do describe the developmental stages according to the vocabulary
extracted from RNA-seq datasets?
● How to progress efficiently? We start now!
11h00-11h30 Coffee break Building C6
11h30-12h30. Preparation of the 2nd general assembly of the COST action


Mario Pezzotti

Anne-Françoise Adam-Blondon

Ana Margarida Fortes

Reinhard Toepfer

Camille Rustenholz

Michele Morgante

Daniela Holtgräwe

Fulvio Mattivi

Jerome Grimplet

José Tomás Matus

Dragan Nikolic

Panagiotis Kalaitzis

Eric Duchêne

Markus Rienth

Doreen Ware (via video conferencing)

Invited Speakers:

Kristina Gruden

Daniel Faria

Alessandro Cestaro

Bjorn Usadel