Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA.
Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA.
Nucleic Acids Res. 2021 Jan 8;49(D1):D1452-D1463. doi: 10.1093/nar/gkaa979.
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.
Gramene（http://www.gramene.org）是一个基于模型植物和主要作物基因组和途径数据的比较功能分析的知识库，为全球农业研究人员提供支持。该资源致力于开放获取和基于 FAIR 数据原则的可重复科学。自上次 NAR 更新以来，我们发布了九个版本；基因组门户的内容增加了一倍；扩展了经过精心整理的基因、途径和表达集；并实施了域信息词汇提取（DIVE）算法，用于从文献中提取基因功能信息。当前版本#63（2020 年 10 月），包含 93 个参考基因组——超过 122947 个家族中的 390 多万个基因，具有同源和旁系分类。植物反应组使用在水稻中的手动生物注释（320 个参考途径）和基于同源性的到 106 个物种的投影的组合来描绘途径网络。Reactome 平台促进了参考和预测途径、基因表达分析以及基因-基因相互作用的覆盖之间的比较。Gramene 集成了基于本体的蛋白质结构-功能注释；遗传、表观遗传、表达和表型多样性信息；以及使用 DIVE 从植物重点期刊中提取的基因功能注释。我们培训植物研究人员进行基因和途径的生物注释；将经过精心整理的玉米基因结构作为玉米基因组浏览器中的轨道进行托管；并将经过精心整理的水稻基因和途径集成到植物反应组中。
