@article{82,
  keywords = {Crops, Agricultural, DNA Transposable Elements, Databases, Genetic, Gene Duplication, Gene Expression Regulation, Plant, Gene Ontology, Gene Regulatory Networks, Genome, Plant, Genomics, Internet, Knowledge Bases, Metabolic Networks and Pathways, Molecular Sequence Annotation, Oryza, Plant Proteins, Plants, Polyploidy, Protein Interaction Mapping, Software, Zea mays},
  author = {Marcela Tello-Ruiz and Sushma Naithani and Parul Gupta and Andrew Olson and Sharon Wei and Justin Preece and Yinping Jiao and Bo Wang and Kapeel Chougule and Priyanka Garg and Justin Elser and Sunita Kumari and Vivek Kumar and Bruno Contreras-Moreira and Guy Naamati and Nancy George and Justin Cook and Daniel Bolser and Peter D'Eustachio and Lincoln Stein and Amit Gupta and Weijia Xu and Jennifer Regala and Irene Papatheodorou and Paul Kersey and Paul Flicek and Crispin Taylor and Pankaj Jaiswal and Doreen Ware},
  title = {Gramene 2021: harnessing the power of comparative genomics and pathways for plant research.},
  abstract = {<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>
},
  year = {2021},
  journal = {Nucleic Acids Res},
  volume = {49},
  pages = {D1452-D1463},
  month = {2021 Jan 08},
  issn = {1362-4962},
  doi = {10.1093/nar/gkaa979},
  language = {eng},
}