ArticleNucleic acids research2024
Planteome 2024 Update: Reference Ontologies and Knowledgebase for Plant Biology.
Article in Nucleic acids research, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed.
- From knowledge graph to topological data analysis: a novel framework to analyze gene regulatory networks for tomato-multi-pathogen interactions.The New phytologist · 2026Article
- CartograPlant: bridging genomic, phenotypic, and environmental data to advance plant resilience and eco-evolutionary insight.Genetics · 2026Article
- The future is FAIR: a community framework for enhanced data management and data sharing.Database : the journal of biological databases and curation · 2026Article
- Improving annotation, access, and comparison of nutritional composition data for underutilized crops.Database : the journal of biological databases and curation · 2026Article
- Gramene 2025: expanded comparative genomics and pathway resources, integrated search, and pan-genome portals for crop research.Nucleic acids research · 2026Article
- Unveiling the diversity and mechanisms of plant growth-promoting bacteria in orchids: a comprehensive review.Frontiers in microbiology · 2026Review
- Comparative genomic analysis of QTL for resistance to Aphanomyces euteiches between pea, lentil, faba bean, and the model species Medicago truncatula.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2025Article
- A curation system of rice trait ontology with reliable interoperation by LLM and PubAnnotation.Genomics & informatics · 2025Article
- GrameneOryza: a comprehensive resource for Oryza genomes, genetic variation, and functional data.Database : the journal of biological databases and curation · 2025Article
- Post-composing ontology terms for efficient phenotyping in plant breeding.Database : the journal of biological databases and curation · 2025Article
- The Unified Phenotype Ontology : a framework for cross-species integrative phenomics.Genetics · 2025Article
- ACT2.6: Global Gene Coexpression Network inGenes · 2025Article
- Building resource-efficient community databases using open-source software.Database : the journal of biological databases and curation · 2025Article
- A conserved fungal Knr4/Smi1 protein is crucial for maintaining cell wall stress tolerance and host plant pathogenesis.PLoS pathogens · 2025Article
- Navigating Amaryllidaceae alkaloids: bridging gaps and charting biosynthetic territories.Journal of experimental botany · 2025Review
- The Unified Phenotype Ontology (uPheno): A framework for cross-species integrative phenomics.bioRxiv : the preprint server for biology · 2024Article
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Authors and funding
5 authors.
Funding
Abstract
The Planteome project (https://planteome.org/) provides a suite of reference and crop-specific ontologies and an integrated knowledgebase of plant genomics data. The plant genomics data in the Planteome has been obtained through manual and automated curation and sourced from more than 40 partner databases and resources. Here, we report on updates to the Planteome reference ontologies, namely, the Plant Ontology (PO), Trait Ontology (TO), the Plant Experimental Conditions Ontology (PECO), and integration of species/crop-specific vocabularies from our partners, the Crop Ontology (CO) into the TO ontology graph. Currently, 11 CO vocabularies are integrated into the Planteome with the addition of yam, sorghum, and potato since 2018. In addition, the size of the annotation database has increased by 34%, and the number of bioentities (genes, proteins, etc.) from 125 plant taxa has increased by 72%. We developed new tools to facilitate user requests and improvements to the CO vocabularies, and to allow fast searching and browsing of PO terms and definitions. These enhancements and future changes to automate the TO-CO mappings and knowledge discovery tools ensure that the Planteome will continue to be a valuable resource for plant biology.
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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.