CorkOakDB—The Cork Oak Genome Database Portal

Abstract

Quercus suber (cork oak) is an evergreen tree native to the Mediterranean basin, which plays a key role in the ecology and economy of this area. Over the last decades, this species has gone through an observable decline, mostly due to environmental factors. Deciphering the mechanisms of cork oak’s response to the environment and getting a deep insight into its biology are crucial to counteract biotic and abiotic stresses compromising the stability of a unique ecosystem. In the light of these setbacks, the publication of the genome in 2018 was a major step towards understanding the genetic make-up of this species. In an effort to integrate this information in a comprehensive, accessible and intuitive format, we have developed The Cork Oak Genome Database Portal (CorkOakDB). The CorkOakDB is supported by the BioData.pt e-infrastructure, the Portuguese ELIXIR node for biological data. The portal gives public access to search and explore the curated genomic and transcriptomic data on this species. Moreover, CorkOakDB provides a user-friendly interface and functional tools to help the research community take advantage of the increased accessibility to genomic information. A study case is provided to highlight the functionalities of the portal. CorkOakDB guarantees the update, curation and data collection, aiming to collect data besides the genetic/genomic information, in order to become the main repository in cork oak research. Database URL: http://corkoakdb.org/

Making European performance and impact assessment frameworks glocal

“…For instance, pathways 5 -Learning and training by using RI facilities and services, 9 -Provision of specifically curated/edited data, and 11 -Creating and shaping scientific networks and communities could be applied in the monitoring the impact of BioData.pt training activities (e.g., "Ready for BioData Management? "), the CorkOak DB portal 13 and the consolidation of our Communities and Platforms, in a multidisciplinary network to identify gaps in computing data management and bioinformatics for the life sciences and build solutions. In these cases, around 50% alignment with the primary indicators of each referred pathway was observed, while only 25% alignment was detected when all BioData.pt project indicators were compared with the overall indicators list.…”

Making European performance and impact assessment frameworks for research infrastructures glocal

“…RI-PATHS also proposes a set of pathways tailored to assess the socio-economic impact of specific project activities, encompassing smaller subgroups of indicators. For instance, pathways 5 - Learning and training by using RI facilities and services , 9 - Provision of specifically curated/edited data , and 11 - Creating and shaping scientific networks and communities seem better suited to evaluate the impact of BioData.pt training activities (e.g., “ Ready for BioData Management ?”), the CorkOak DB portal, 13 and the “building and consolidation of our Communities and Platforms, in a multidisciplinary network to identify gaps in computing data management and bioinformatics for the life sciences and build solutions”.…”

“…The missing indicator, Number of publicly available data sets used externally, relates to the optimisation of data use and is a relevant indicator for a RI like BioData.pt. Although BioData.pt has publicly available datasets (e.g., Pheno and CorkOakDB 13 ), it does not currently maintain indicators to demonstrate how these are being used externally. This difficulty also intricates with the fact that there is still a long way to go in the formal acknowledgement of RI services by its users, which is harder when the goods provided are intangible and sometimes provided by third parties.…”

Genome‐wide identification, phylogeny, and gene duplication of the epigenetic regulators in Fagaceae

“…F. sylvatica, F. crenata, Castanea henryi (Skan) Rehder & E.H. Wilson, and C. crenata. Q. suber transcriptome data were retrieved from the Cork Oak DB (Arias-Baldrich et al, 2020). The accession numbers from SRA raw-sequencing data used can be found in Table S2.…”