Tello-Ruiz, M. K., Naithani, S., Gupta, P., Olson, A., Wei, S., Preece, J., Jiao, Y., Wang, B., Chougule, K., Garg, P., Elser, J., Kumari, S., Kumar, V., Contreras-Moreira, B., Naamati, G., George, N., Cook, J., Bolser, D., D'Eustachio, P., Stein, L. D., Gupta, A., Xu, W., Regala, J., Papatheodorou, I., Kersey, P. J., Flicek, P., Taylor, C., Jaiswal, P., Ware, D. (January 2021) Gramene 2021: harnessing the power of comparative genomics and pathways for plant research. Nucleic Acids Res, 49 (D1). D1452-d1463. ISSN 0305-1048 (Print)0305-1048
Abstract
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.
| Item Type: | Paper |
|---|---|
| Additional Information: | 1362-4962 Tello-Ruiz, Marcela K Naithani, Sushma Gupta, Parul Olson, Andrew Wei, Sharon Preece, Justin Jiao, Yinping Wang, Bo Chougule, Kapeel Garg, Priyanka Elser, Justin Kumari, Sunita Kumar, Vivek Contreras-Moreira, Bruno Naamati, Guy George, Nancy Cook, Justin Bolser, Daniel D'Eustachio, Peter Stein, Lincoln D Gupta, Amit Xu, Weijia Regala, Jennifer Papatheodorou, Irene Kersey, Paul J Flicek, Paul Taylor, Crispin Jaiswal, Pankaj Ware, Doreen P41 HG003751/HG/NHGRI NIH HHS/United States U41 HG003751/HG/NHGRI NIH HHS/United States Journal Article Nucleic Acids Res. 2021 Jan 8;49(D1):D1452-D1463. doi: 10.1093/nar/gkaa979. |
| Subjects: | bioinformatics bioinformatics > genomics and proteomics > genetics & nucleic acid processing bioinformatics > genomics and proteomics organism description > plant > Oryza organism description > plant behavior bioinformatics > genomics and proteomics > genetics & nucleic acid processing > protein structure, function, modification organism description > plant behavior > crop yield improvement bioinformatics > genomics and proteomics > genetics & nucleic acid processing > genomes organism description > plant bioinformatics > genomics and proteomics > genetics & nucleic acid processing > protein structure, function, modification > protein types > plant proteins bioinformatics > genomics and proteomics > genetics & nucleic acid processing > protein structure, function, modification > protein types |
| CSHL Authors: | |
| Communities: | CSHL labs > Ware lab |
| Depositing User: | Matthew Dunn |
| Date: | 8 January 2021 |
| Date Deposited: | 11 Jan 2021 15:53 |
| Last Modified: | 25 Jan 2024 19:35 |
| PMCID: | PMC7779000 |
| Related URLs: | |
| URI: | https://repository.cshl.edu/id/eprint/39893 |
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