CorkOakDB-The Cork Oak Genome Database Portal.
Journal
Database : the journal of biological databases and curation
ISSN: 1758-0463
Titre abrégé: Database (Oxford)
Pays: England
ID NLM: 101517697
Informations de publication
Date de publication:
31 12 2020
31 12 2020
Historique:
received:
19
08
2020
revised:
04
12
2020
accepted:
11
12
2020
entrez:
31
12
2020
pubmed:
1
1
2021
medline:
28
10
2021
Statut:
ppublish
Résumé
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/.
Identifiants
pubmed: 33382885
pii: 6056470
doi: 10.1093/database/baaa114
pmc: PMC7774466
pii:
doi:
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Informations de copyright
© The Author(s) 2020. Published by Oxford University Press.
Références
Curr Protoc Bioinformatics. 2010 Dec;Chapter 9:Unit 9.13
pubmed: 21154710
Nucleic Acids Res. 2014 Jan;42(Database issue):D1229-36
pubmed: 24203703
Front Plant Sci. 2014 Nov 06;5:599
pubmed: 25414713
BMC Genomics. 2014 May 15;15:371
pubmed: 24885229
Database (Oxford). 2013 May 23;2013:bat035
pubmed: 23707967
BMC Plant Biol. 2015 Jun 25;15:158
pubmed: 26109289
Plant J. 2020 May;102(3):431-447
pubmed: 32027440
Planta. 2018 Feb;247(2):317-338
pubmed: 28988391
BMC Bioinformatics. 2010 Jun 23;11:341
pubmed: 20573248
Nat Methods. 2015 Apr;12(4):357-60
pubmed: 25751142
J Mol Biol. 1990 Oct 5;215(3):403-10
pubmed: 2231712
Nucleic Acids Res. 1998 Jan 1;26(1):73-9
pubmed: 9399804
Sci Data. 2018 May 22;5:180069
pubmed: 29786699
Bioinformatics. 2014 Aug 1;30(15):2114-20
pubmed: 24695404
Trends Plant Sci. 2010 Oct;15(10):573-81
pubmed: 20674465
Curr Protoc Bioinformatics. 2006 Jan;Chapter 9:Unit 9.6
pubmed: 18428772
New Phytol. 2020 Jul;227(1):260-273
pubmed: 32171029
Nat Biotechnol. 2015 Mar;33(3):290-5
pubmed: 25690850
Plant Mol Biol. 2018 Jan;96(1-2):103-118
pubmed: 29143299
Bioinformatics. 2019 Oct 15;35(20):4147-4155
pubmed: 30903186
Nucleic Acids Res. 1992 May 11;20 Suppl:2019-22
pubmed: 1598233
J Exp Bot. 2014 Sep;65(17):4887-905
pubmed: 24958897
Nucleic Acids Res. 2011 Jan;39(Database issue):D19-21
pubmed: 21062823
Front Plant Sci. 2016 Jan 11;6:1195
pubmed: 26793200
Tree Physiol. 2020 Feb 20;40(2):129-141
pubmed: 31860724
Database (Oxford). 2017 Jan 1;2017:
pubmed: 29220446
Nucleic Acids Res. 2019 Jan 8;47(D1):D1137-D1145
pubmed: 30357347
Genome Biol. 2016 Apr 12;17:66
pubmed: 27072794
Bioinformatics. 2005 May 1;21(9):1859-75
pubmed: 15728110
Plant J. 2020 Jul;103(2):660-676
pubmed: 32246506
Database (Oxford). 2019 Jan 1;2019:
pubmed: 31328773
Nucleic Acids Res. 2012 Jan;40(Database issue):D57-63
pubmed: 22139929