Gramene 2021: harnessing the power of comparative genomics and pathways for plant research.
Crops, Agricultural
DNA Transposable Elements
Databases, Genetic
Gene Duplication
Gene Expression Regulation, Plant
Gene Ontology
Gene Regulatory Networks
Genome, Plant
Genomics
/ methods
Internet
Knowledge Bases
Metabolic Networks and Pathways
Molecular Sequence Annotation
Oryza
/ genetics
Plant Proteins
/ genetics
Plants
/ classification
Polyploidy
Protein Interaction Mapping
Software
Zea mays
/ genetics
Journal
Nucleic acids research
ISSN: 1362-4962
Titre abrégé: Nucleic Acids Res
Pays: England
ID NLM: 0411011
Informations de publication
Date de publication:
08 01 2021
08 01 2021
Historique:
accepted:
09
10
2020
received:
15
09
2020
pubmed:
11
11
2020
medline:
27
1
2021
entrez:
10
11
2020
Statut:
ppublish
Résumé
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.
Identifiants
pubmed: 33170273
pii: 5973447
doi: 10.1093/nar/gkaa979
pmc: PMC7779000
doi:
Substances chimiques
DNA Transposable Elements
0
Plant Proteins
0
Types de publication
Journal Article
Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, Non-P.H.S.
Langues
eng
Sous-ensembles de citation
IM
Pagination
D1452-D1463Subventions
Organisme : NHGRI NIH HHS
ID : P41 HG003751
Pays : United States
Organisme : NHGRI NIH HHS
ID : U41 HG003751
Pays : United States
Organisme : Biotechnology and Biological Sciences Research Council
ID : BB/P016855/1
Pays : United Kingdom
Organisme : Wellcome Trust
ID : 108437/Z/15/Z
Pays : United Kingdom
Organisme : Wellcome Trust
ID : WT101477MA
Pays : United Kingdom
Informations de copyright
Published by Oxford University Press on behalf of Nucleic Acids Research 2020.
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