Global Omic Data Integration on Animal, Vegetal and Environment Sectors

Información del proyecto

GLOMICAVE

Identificador del acuerdo de subvención: 952908

DOI

10.3030/952908

Proyecto cerrado

Fecha de la firma de la CE 9 Noviembre 2020

Fecha de inicio 1 Noviembre 2020

Fecha de finalización 30 Abril 2024

Financiado con arreglo a

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

Coste total

€ 6 372 583,75

Aportación de la UE

€ 6 372 583,75

Coordinado por

FUNDACIO EURECAT
Spain

CORDIS proporciona enlaces a los documentos públicos y las publicaciones de los proyectos de los programas marco HORIZONTE.

Los enlaces a los documentos y las publicaciones de los proyectos del Séptimo Programa Marco, así como los enlaces a algunos tipos de resultados específicos, como conjuntos de datos y «software», se obtienen dinámicamente de OpenAIRE .

Resultado final

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.

Publicaciones

Non-peer reviewed articles (6)

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

Autores: Isabel Gimeno; Pablo García-Manrique; Susana Carrocera; Cristina López-Hidalgo; Luis Valledor; David Martín-González; Enrique J. Gómez
Publicado en: Metabolites, Edición 2, 2021, Página(s) 484, ISSN 2218-1989
Editor: MDPI
DOI: 10.3390/metabo11080484

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

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

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

Autores: 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.
Publicado en: New Phytologist, 2022, ISSN 1469-8137
Editor: Wiley
DOI: 10.1111/nph.18095

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

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

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

Autores: Gimeno, I., Salvetti, P., Carrocera, S., Gatien, J., García-Manrique, P., López-Hidalgo, C., Valledor, L., Gómez, E
Publicado en: Journal of dairy science, 2023, ISSN 0022-0302
Editor: 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

Autores: Sequeira, J. C.; Rocha, Miguel; Alves, M. M.; Salvador, Andreia Filipa Ferreira
Publicado en: Computational and Structural Biotechnology Journal, Edición 1, 2022, Página(s) 1798-1810, ISSN 2001-0370
Editor: Elsevier
DOI: 10.1016/j.csbj.2022.03.042

Peer reviewed articles (4)

Computational Expansion of High-Resolution-MSn Spectral Libraries

Autores: 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)
Publicado en: Analytical Chemistry, 2023, ISSN 1520-6882
Editor: 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

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

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

Autores: 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).
Publicado en: The Plant Journal, 2023, 2023, ISSN 1365-313X
Editor: 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

Autores: 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)
Publicado en: New Phytologist, Edición Volume 240, 2023, ISSN 1469-8137
Editor: New Phytologist Foundation
DOI: 10.1111/nph.19160