ArticleDatabase : the journal of biological databases and curation2025
GrameneOryza: a comprehensive resource for Oryza genomes, genetic variation, and functional data.
Article in Database : the journal of biological databases and curation, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
2 citing papers in PubMed.
- Adoption of Standard Reference SNP Identifiers in Agricultural Genomics for Interoperability and Data Reuse.Scientific data · 2026Article
- Gramene 2025: expanded comparative genomics and pathway resources, integrated search, and pan-genome portals for crop research.Nucleic acids research · 2026Article
Corrections and comments
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Authors and funding
12 authors.
Funding
Abstract
Rice is a vital staple crop, sustaining over half of the global population, and is a key model for genetic research. To support the growing need for comprehensive and accessible rice genomic data, GrameneOryza (https://oryza.gramene.org) was developed as an online resource adhering to FAIR (Findable, Accessible, Interoperable, and Reusable) principles of data management. It distinguishes itself through its comprehensive multispecies focus, encompassing a wide variety of Oryza genomes and related species, and its integration with FAIR principles to ensure data accessibility and usability. It offers a community curated selection of high-quality Oryza genomes, genetic variation, gene function, and trait data. The latest release, version 8, includes 28 Oryza genomes, covering wild rice and domesticated cultivars. These genomes, along with Leersia perrieri and seven additional outgroup species, form the basis for 38 K protein-coding gene family trees, essential for identifying orthologs, paralogs, and developing pan-gene sets. GrameneOryza's genetic variation data features 66 million single-nucleotide variants (SNVs) anchored to the Os-Nipponbare-Reference-IRGSP-1.0 genome, derived from various studies, including the Rice Genome 3 K (RG3K) project. The RG3K sequence reads were also mapped to seven additional platinum-quality Asian rice genomes, resulting in 19 million SNVs for each genome, significantly expanding the coverage of genetic variation beyond the Nipponbare reference. Of the 66 million SNVs on IRGSP-1.0, 27 million acquired standardized reference SNP cluster identifiers (rsIDs) from the European Variation Archive release v5. Additionally, 1200 distinct phenotypes provide a comprehensive overview of quantitative trait loci (QTL) features. The newly introduced Oryza CLIMtools portal offers insights into environmental impacts on genome adaptation. The platform's integrated search interface, along with a BLAST server and curation tools, facilitates user access to genomic, phylogenetic, gene function, and QTL data, supporting broad research applications. Database URL: https://oryza.gramene.org.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.