Global Omic Data Integration on Animal, Vegetal and Environment Sectors

Deliverables

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

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

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

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

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

Author(s): Isabel Gimeno; Pablo García-Manrique; Susana Carrocera; Cristina López-Hidalgo; Luis Valledor; David Martín-González; Enrique J. Gómez
Published in: Metabolites, Issue 2, 2021, Page(s) 484, ISSN 2218-1989
Publisher: MDPI
DOI: 10.3390/metabo11080484

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

Author(s): Gómez Enrique, Murillo Antonio, Carrocera Susana, Pérez-Jánez Juan José, Benedito Jose Luis, Martín-González David, Gimeno Isabel
Published in: Frontiers in Veterinary Science, 2022, ISSN 2297-1769
Publisher: -
DOI: 10.3389/fvets.2022.1006995

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

Author(s): 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.
Published in: New Phytologist, 2022, ISSN 1469-8137
Publisher: Wiley
DOI: 10.1111/nph.18095

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

Author(s): Sara M. de Cripan, Adrià Cereto-Massagué, Pol Herrero, Andrei Barcaru, Núria Canela, & Xavier Domingo-Almenara
Published in: Biomedicines, Special Issue Omics Data Analysis and Integration in Complex Diseases, 2022, ISSN 2227-9059
Publisher: MDPI
DOI: 10.3390/biomedicines10040879

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

Author(s): Gimeno, I., Salvetti, P., Carrocera, S., Gatien, J., García-Manrique, P., López-Hidalgo, C., Valledor, L., Gómez, E
Published in: Journal of dairy science, 2023, ISSN 0022-0302
Publisher: 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

Author(s): Sequeira, J. C.; Rocha, Miguel; Alves, M. M.; Salvador, Andreia Filipa Ferreira
Published in: Computational and Structural Biotechnology Journal, Issue 1, 2022, Page(s) 1798-1810, ISSN 2001-0370
Publisher: Elsevier
DOI: 10.1016/j.csbj.2022.03.042

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

Author(s): 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)
Published in: New Phytologist, Issue Volume 240, 2023, ISSN 1469-8137
Publisher: New Phytologist Foundation
DOI: 10.1111/nph.19160

Deliverables

Publications

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