Global Omic Data Integration on Animal, Vegetal and Environment Sectors

Informations projet

GLOMICAVE

N° de convention de subvention: 952908

DOI

10.3030/952908

Projet clôturé

Date de signature de la CE 9 Novembre 2020

Date de début 1 Novembre 2020

Date de fin 30 Avril 2024

Financé au titre de

• INDUSTRIAL LEADERSHIP - Leadership in enabling and industrial technologies – Biotechnology

Coût total

€ 6 372 583,75

Contribution de l’UE

€ 6 372 583,75

Coordonné par

FUNDACIO EURECAT
Spain

CORDIS fournit des liens vers les livrables publics et les publications des projets HORIZON.

Les liens vers les livrables et les publications des projets du 7e PC, ainsi que les liens vers certains types de résultats spécifiques tels que les jeux de données et les logiciels, sont récupérés dynamiquement sur OpenAIRE .

Livrables

Documents, reports (6)

GLOMICAVE semantic model

Common vocabulary to represent omic data and experiments to facilitate data integration and exploration

Responsible research and innovation

Reporting evidence on direct RRI actions carried out by the project.

Novel training Dataset and labelling functions

Report explaining the fundamentals to be able to automatically label the scientific text downloaded to allow the automatic preprocessing of the literature

Report on the contribution to standardization

Description of the objectives methodology and results that refer to the collaboration and communication with the relevant standardization Technical Committees of the standardization system and the contribution of GLOMICAVE to the ongoing and future standardization development

Report on the standardization landscape and applicable standards

Report presenting the project related applicable existing standards

Datasets and repositories benchmarking

Deliverable devoted to assess the different repositories and datasets to derive data model and integration requirements

Demonstrators, pilots, prototypes (5)

GLOMICAVE Knowledge graph

Development of a semantic repository and subsequent plugins to store experiment information and metadata

"GLOMICAVE pre-operational consolidated platform - ""beta"" release"

Overview of GLOMICAVE integrative approach including guidelines of installation.

GLOMICAVE Data lake

Consolidated version of the GLOMICAVE data lake including plug-ins, data curation mechanism and the specifications of the Open-API.

GLOMICAVE Open API

Details on how GLOMICAVE will facilitate data visualization and also data interaction with the rest of the analytical services.

Data gathering and curation mechanisms

Development of a curated data structure for experiment metadata and webbased interface to collaboratively curate submitted datasets and link datasets to shared internal or external identifiers

Other (3)

GLOMICAVE website

Launch of the project public webpage for communication and dissemination purposes Report describing the website and the main functionalities

Public Communication Materials

First collection of public materials to be used for communication purposes

Final Public Communication Materials

Final collection of public materials prepared for communication purposes.

Publications

Non-peer reviewed articles (6)

The Metabolic Signature of In Vitro Produced Bovine Embryos Helps Predict Pregnancy and Birth after Embryo Transfer.

Auteurs: Isabel Gimeno; Pablo García-Manrique; Susana Carrocera; Cristina López-Hidalgo; Luis Valledor; David Martín-González; Enrique J. Gómez
Publié dans: Metabolites, Numéro 2, 2021, Page(s) 484, ISSN 2218-1989
Éditeur: MDPI
DOI: 10.3390/metabo11080484

Fitness of calves born from in vitro-produced fresh and cryopreserved embryos

Auteurs: Gómez Enrique, Murillo Antonio, Carrocera Susana, Pérez-Jánez Juan José, Benedito Jose Luis, Martín-González David, Gimeno Isabel
Publié dans: Frontiers in Veterinary Science, 2022, ISSN 2297-1769
Éditeur: -
DOI: 10.3389/fvets.2022.1006995

Predictive metabolomics of multiple Atacama plant species unveils a core set of generic metabolites for extreme climate resilience

Auteurs: 2. Dussarrat, T., Prigent, S., Latorre, C., Bernillon, S., Flandin, A., Díaz, F.P., Cassan, C., Van Delft, P., Jacob, D., Varala, K., Joubes, J., Gibon, Y., Rolin, D., Gutiérrez, R.A. and Pétriacq, P.
Publié dans: New Phytologist, 2022, ISSN 1469-8137
Éditeur: Wiley
DOI: 10.1111/nph.18095

Machine Learning-Based Retention Time Prediction of Trimethylsilyl Derivatives of Metabolites

Auteurs: Sara M. de Cripan, Adrià Cereto-Massagué, Pol Herrero, Andrei Barcaru, Núria Canela, & Xavier Domingo-Almenara
Publié dans: Biomedicines, Special Numéro Omics Data Analysis and Integration in Complex Diseases, 2022, ISSN 2227-9059
Éditeur: MDPI
DOI: 10.3390/biomedicines10040879

Biomarker metabolite mating of viable frozen-thawed IVP bovine embryos with pregnancy-competent recipients leads to improved birth rates

Auteurs: Gimeno, I., Salvetti, P., Carrocera, S., Gatien, J., García-Manrique, P., López-Hidalgo, C., Valledor, L., Gómez, E
Publié dans: Journal of dairy science, 2023, ISSN 0022-0302
Éditeur: American Dairy Science Association
DOI: 10.3168/jds.2022-23082

UPIMAPI, reCOGnizer and KEGGCharter: Bioinformatics tools for functional annotation and visualization of (meta)-omics datasets

Auteurs: Sequeira, J. C.; Rocha, Miguel; Alves, M. M.; Salvador, Andreia Filipa Ferreira
Publié dans: Computational and Structural Biotechnology Journal, Numéro 1, 2022, Page(s) 1798-1810, ISSN 2001-0370
Éditeur: Elsevier
DOI: 10.1016/j.csbj.2022.03.042

Peer reviewed articles (4)

Computational Expansion of High-Resolution-MSn Spectral Libraries

Auteurs: by Brandon Y. Lieng; Andrew T. Quaile; Hannes L. Rös (Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto); Xavier Domingo-Almenara (Centre for Omics Sciences, Eurecat – Technology Centre of Catalonia & Rovira i Virgili University Joint Unit)
Publié dans: Analytical Chemistry, 2023, ISSN 1520-6882
Éditeur: ACS Publications
DOI: 10.1021/acs.analchem.3c03343

The recipient metabolome explains the asymmetric ovarian impact on fetal sex development after embryo transfer in cattle

Auteurs: by Isabel Gimeno; Susana Carrocera; Enrique Gómez (Servicio Regional de Investigación y Desarrollo Agroalimentario); Pascal Salvetti; Julie Gatien & Daniel Le Bourhis (ELIANCE)
Publié dans: Journal of Animal Science, 2024, ISSN 1525-3163
Éditeur: Oxford Academic
DOI: 10.1093/jas/skae081

Comparative constraint-based modelling of fruitdevelopment across species highlights nitrogen metabolismin the growth-defence trade-off

Auteurs: by Sophie Colombie, Sylvain Prigent, Cedric Cassan, Annick Moing, Chloe Beaumont, Bertrand Beauvoit, Yves Gibon, Ghislaine Hilbert-Masson, Christel Renaud (Univ. Bordeaux), Emilia Dell’Aversana, Petronia Carillo (University of Campania “Luigi Vanvitelli”), Tim McCubbin, and Lars Keld Nielsen (The University of Queensland).
Publié dans: The Plant Journal, 2023, 2023, ISSN 1365-313X
Éditeur: Wiley Online Library
DOI: 10.1111/tpj.16409

Enzyme-based kinetic modelling of ASC–GSH cycle during tomato fruit development reveals the importance of reducing power and ROS availability

Auteurs: by Guillaume Decros; Thomas Dussarrat; Pierre Baldet; Martine Dieuaide-Noubhani; Alice Destailleur; Sylvain Prigent; Kentaro Mori; Joana Jorly; Sophie Colombié; Bertrand Beauvoit (INRAE, University of Bordeaux); Yves Gibon; Cédric Cassan; Amélie Flandin; Cécile Cabasson; Pierre Pétriacq (Bordeaux Metabolome, MetaboHUB)
Publié dans: New Phytologist, Numéro Volume 240, 2023, ISSN 1469-8137
Éditeur: New Phytologist Foundation
DOI: 10.1111/nph.19160