03373nas a2200721   4500000000100000000000100001008004100002260001600043653002400059653003000083653002300113653002100136653003800157653001800195653002900213653001800242653001300260653001300273653002000286653003600306653003400342653001000376653001900386653001100405653001500416653003200431653001300463653001300476100002300489700002000512700001600532700001700548700001500565700001800580700001700598700001200615700002000627700001800647700001700665700001800682700001600700700002800716700001600744700001700760700001600777700001800793700002200811700001800833700001500851700001400866700002000880700002400900700001600924700001600940700001900956700001900975700001600994245009601010300001601106490000701122520150801129022001402637       2021                            d  c2021 Jan 0810aCrops, Agricultural10aDNA Transposable Elements10aDatabases, Genetic10aGene Duplication10aGene Expression Regulation, Plant10aGene Ontology10aGene Regulatory Networks10aGenome, Plant10aGenomics10aInternet10aKnowledge Bases10aMetabolic Networks and Pathways10aMolecular Sequence Annotation10aOryza10aPlant Proteins10aPlants10aPolyploidy10aProtein Interaction Mapping10aSoftware10aZea mays1 aMarcela Tello-Ruiz1 aSushma Naithani1 aParul Gupta1 aAndrew Olson1 aSharon Wei1 aJustin Preece1 aYinping Jiao1 aBo Wang1 aKapeel Chougule1 aPriyanka Garg1 aJustin Elser1 aSunita Kumari1 aVivek Kumar1 aBruno Contreras-Moreira1 aGuy Naamati1 aNancy George1 aJustin Cook1 aDaniel Bolser1 aPeter D'Eustachio1 aLincoln Stein1 aAmit Gupta1 aWeijia Xu1 aJennifer Regala1 aIrene Papatheodorou1 aPaul Kersey1 aPaul Flicek1 aCrispin Taylor1 aPankaj Jaiswal1 aDoreen Ware00aGramene 2021: harnessing the power of comparative genomics and pathways for plant research.  aD1452-D14630 v493 a<p>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.</p>
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