TY - JOUR
T1 - Gramene 2021: harnessing the power of comparative genomics and pathways for plant research
T2 - Harnessing the power of comparative genomics and pathways for plant research
AU - Tello-Ruiz, Marcela K
AU - Naithani, Sushma
AU - Gupta, Parul
AU - Olson, Andrew
AU - Wei, Sharon
AU - Preece, Justin
AU - Jiao, Yinping
AU - Wang, Bo
AU - Chougule, Kapeel
AU - Garg, Priyanka
AU - Elser, Justin
AU - Kumari, Sunita
AU - Kumar, Vivek
AU - Contreras-Moreira, Bruno
AU - Naamati, Guy
AU - George, Nancy
AU - Cook, Justin
AU - Bolser, Daniel
AU - D'Eustachio, Peter
AU - Stein, Lincoln D.
AU - Gupta, Amit
AU - Xu, Weijia
AU - Regala, Jennifer
AU - Papatheodorou, Irene
AU - Kersey, Paul J.
AU - Flicek, Paul
AU - Taylor, Crispin
AU - Jaiswal, Pankaj
AU - Ware, Doreen
N1 - Funding Information:
National Science Foundation (NSF) [IOS-1127112, IOS-1340112]; United States Department of Agriculture - Agricultural Research Service [58-1907- 4-030, 8062-21000-041-00D to D.W., 52930113 to P.J.]; United Kingdom Biotechnology and Biosciences Research Council [BB/P016855/1 and Ensembl-4-Breeders workshop support]; European Molecular Biology Laboratory; The in-kind infrastructure and intellectual support for the development and running of the Plant Reactome is supported by the Reactome database project via a grant from the US National Institutes of Health [U41 HG003751 to L.S.]; EU grant [LSHG-CT-2005-518254]; 'ENFIN', the Ontario Research Fund; EMBL-EBI Industry Programme; Hosting of the Plant Reactome website on Cyverse was also supported by the NSF [IOS-1743442]; The Expression ATLAS received additional funding form the Single-Cell Gene Expression Atlas and 'PRIDE Atlas' grants from Wellcome [108437/Z/15/Z, WT101477MA to I.P.]; Open Targets; Chan-Zuckerberg Initiative; Ensembl Plants received additional funding from ELIXIR implementation studies FONDUE and 'Apple as a Model for Genomic Information Exchange'; OSU provided partial support for trainee undergraduate students and project personnel at the university. Funding for open access charge: NSF [IOS-1127112].
Publisher Copyright:
© 2021 Published by Oxford University Press on behalf of Nucleic Acids Research 2020.
PY - 2021/1/8
Y1 - 2021/1/8
N2 - Gramene (http://www.gramene.org), a knowledgebase founded on comparative functional analyses of genomic and pathway data for model plants and major crops, supports agricultural researchers worldwide. The resource is committed to open access and reproducible science based on the FAIR data principles. Since the last NAR update, we made nine releases; doubled the genome portal's content; expanded curated genes, pathways and expression sets; and implemented the Domain Informational Vocabulary Extraction (DIVE) algorithm for extracting gene function information from publications. The current release, #63 (October 2020), hosts 93 reference genomes - over 3.9 million genes in 122 947 families with orthologous and paralogous classifications. Plant Reactome portrays pathway networks using a combination of manual biocuration in rice (320 reference pathways) and orthology-based projections to 106 species. The Reactome platform facilitates comparison between reference and projected pathways, gene expression analyses and overlays of gene-gene interactions. Gramene integrates ontology-based protein structure-function annotation; information on genetic, epigenetic, expression, and phenotypic diversity; and gene functional annotations extracted from plant-focused journals using DIVE. We train plant researchers in biocuration of genes and pathways; host curated maize gene structures as tracks in the maize genome browser; and integrate curated rice genes and pathways in the Plant Reactome.
AB - Gramene (http://www.gramene.org), a knowledgebase founded on comparative functional analyses of genomic and pathway data for model plants and major crops, supports agricultural researchers worldwide. The resource is committed to open access and reproducible science based on the FAIR data principles. Since the last NAR update, we made nine releases; doubled the genome portal's content; expanded curated genes, pathways and expression sets; and implemented the Domain Informational Vocabulary Extraction (DIVE) algorithm for extracting gene function information from publications. The current release, #63 (October 2020), hosts 93 reference genomes - over 3.9 million genes in 122 947 families with orthologous and paralogous classifications. Plant Reactome portrays pathway networks using a combination of manual biocuration in rice (320 reference pathways) and orthology-based projections to 106 species. The Reactome platform facilitates comparison between reference and projected pathways, gene expression analyses and overlays of gene-gene interactions. Gramene integrates ontology-based protein structure-function annotation; information on genetic, epigenetic, expression, and phenotypic diversity; and gene functional annotations extracted from plant-focused journals using DIVE. We train plant researchers in biocuration of genes and pathways; host curated maize gene structures as tracks in the maize genome browser; and integrate curated rice genes and pathways in the Plant Reactome.
UR - http://www.scopus.com/inward/record.url?scp=85099428159&partnerID=8YFLogxK
U2 - 10.1093/nar/gkaa979
DO - 10.1093/nar/gkaa979
M3 - Article
C2 - 33170273
SN - 0305-1048
VL - 49
SP - D1452-D1463
JO - Default journal
JF - Default journal
IS - D1
ER -