ArticleComparative and functional genomics2002
Gramene: development and integration of trait and gene ontologies for rice.
Article in Comparative and functional genomics, 2002. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 38 papers.
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Who cites it
38 citing papers in PubMed.
- RGPA-GCN: Graph convolutional networks for rice gene-phenotype association prediction.Plant biology (Stuttgart, Germany) · 2026Article
- A curation system of rice trait ontology with reliable interoperation by LLM and PubAnnotation.Genomics & informatics · 2025Article
- Establishing a Common Nutritional Vocabulary - From Food Production to Diet.Frontiers in nutrition · 2022Article
- Gramene 2021: harnessing the power of comparative genomics and pathways for plant research.Nucleic acids research · 2021Article
- PathBIX-a web server for network-based pathway annotation with adaptive null models.Bioinformatics advances · 2021Article
- Identification of Potential Cytokinin Responsive Key Genes in Rice Treated With Trans-Zeatin Through Systems Biology Approach.Frontiers in genetics · 2021Article
- WTO, an ontology for wheat traits and phenotypes in scientific publications.Genomics & informatics · 2020Article
- Mapping and breeding value evaluation of a semi-dominant semi-dwarf gene in upland rice.Plant diversity · 2018Article
- Survey of Candidate Genes for Maize Resistance to Infection by Aspergillus flavus and/or Aflatoxin Contamination.Toxins · 2018Article
- The Planteome database: an integrated resource for reference ontologies, plant genomics and phenomics.Nucleic acids research · 2018Article
- Suppressive effect of microRNA319 expression on rice plant height.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2017Article
- LEAFDATA: a literature-curated database for Arabidopsis leaf development.Plant methods · 2016Article
- Microarray Meta-Analysis Focused on the Response of Genes Involved in Redox Homeostasis to Diverse Abiotic Stresses in Rice.Frontiers in plant science · 2015Article
- Article
- Manually curated database of rice proteins.Nucleic acids research · 2014Article
- Genome-wide binding analysis of the transcription activator ideal plant architecture1 reveals a complex network regulating rice plant architecture.The Plant cell · 2013Article
- Sustained-input switches for transcription factors and microRNAs are central building blocks of eukaryotic gene circuits.Genome biology · 2013Article
- An integrative, translational approach to understanding rare and orphan genetically based diseases.Interface focus · 2013Article
- The plant ontology as a tool for comparative plant anatomy and genomic analyses.Plant & cell physiology · 2013Article
- A systems-genetics approach and data mining tool to assist in the discovery of genes underlying complex traits in Oryza sativa.PloS one · 2013Article
Corrections and comments
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Authors and funding
12 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Gramene (http://www.gramene.org/) is a comparative genome database for cereal crops and a community resource for rice. We are populating and curating Gramene with annotated rice (Oryza sativa) genomic sequence data and associated biological information including molecular markers, mutants, phenotypes, polymorphisms and Quantitative Trait Loci (QTL). In order to support queries across various data sets as well as across external databases, Gramene will employ three related controlled vocabularies. The specific goal of Gramene is, first to provide a Trait Ontology (TO) that can be used across the cereal crops to facilitate phenotypic comparisons both within and between the genera. Second, a vocabulary for plant anatomy terms, the Plant Ontology (PO) will facilitate the curation of morphological and anatomical feature information with respect to expression, localization of genes and gene products and the affected plant parts in a phenotype. The TO and PO are both in the early stages of development in collaboration with the International Rice Research Institute, TAIR and MaizeDB as part of the Plant Ontology Consortium. Finally, as part of another consortium comprising macromolecular databases from other model organisms, the Gene Ontology Consortium, we are annotating the confirmed and predicted protein entries from rice using both electronic and manual curation.
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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.