ArticleFrontiers in plant science2019
The Plant Ontology Facilitates Comparisons of Plant Development Stages Across Species.
Article in Frontiers in plant science, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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20 citing papers in PubMed.
- Chemical Ontogeny in Plants: Developmental Dynamics of Specialized Metabolism and Implications for Ecology, Quality Control, and Bioprospecting.Plants (Basel, Switzerland) · 2026Review
- Ontology-driven dual-channel relational graph convolutional network (DCR-GCN) for lettuce leaf phenotype classification.Plant methods · 2026Article
- Improving annotation, access, and comparison of nutritional composition data for underutilized crops.Database : the journal of biological databases and curation · 2026Article
- The Gene Ontology knowledgebase in 2026.Nucleic acids research · 2026Article
- Definition of reproductive structures in Eucalyptus for phenological data collection.International journal of biometeorology · 2025Review
- AgroLD: a knowledge graph for the plant sciences.BMC genomic data · 2025Article
- GrameneOryza: a comprehensive resource for Oryza genomes, genetic variation, and functional data.Database : the journal of biological databases and curation · 2025Article
- Planteome 2024 Update: Reference Ontologies and Knowledgebase for Plant Biology.Nucleic acids research · 2024Article
- Plant Reactome Knowledgebase: empowering plant pathway exploration and OMICS data analysis.Nucleic acids research · 2024Article
- Exploring Pan-Genomes: An Overview of Resources and Tools for Unraveling Structure, Function, and Evolution of Crop Genes and Genomes.Biomolecules · 2023Review
- Article
- A phenomics approach reveals interspecific differences in integrated developmental responses to chronic elevated temperatures.The Journal of experimental biology · 2023Article
- The Gene Ontology knowledgebase in 2023.Genetics · 2023Review
- Toward a data infrastructure for the Plant Cell Atlas.Plant physiology · 2023Review
- Comparative phenomics: a new approach to study heterochrony.Frontiers in physiology · 2023Article
- Using knowledge graphs to infer gene expression in plants.Frontiers in artificial intelligence · 2023Article
- Ontologies for increasing the FAIRness of plant research data.Frontiers in plant science · 2023Review
- The Ontologies Community of Practice: A CGIAR Initiative for Big Data in Agrifood Systems.Patterns (New York, N.Y.) · 2020Article
- ProteomicsDB: a multi-omics and multi-organism resource for life science research.Nucleic acids research · 2020Article
- Article
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8 authors.
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Abstract
The Plant Ontology (PO) is a community resource consisting of standardized terms, definitions, and logical relations describing plant structures and development stages, augmented by a large database of annotations from genomic and phenomic studies. This paper describes the structure of the ontology and the design principles we used in constructing PO terms for plant development stages. It also provides details of the methodology and rationale behind our revision and expansion of the PO to cover development stages for all plants, particularly the land plants (bryophytes through angiosperms). As a case study to illustrate the general approach, we examine variation in gene expression across embryo development stages in Arabidopsis and maize, demonstrating how the PO can be used to compare patterns of expression across stages and in developmentally different species. Although many genes appear to be active throughout embryo development, we identified a small set of uniquely expressed genes for each stage of embryo development and also between the two species. Evaluating the different sets of genes expressed during embryo development in Arabidopsis or maize may inform future studies of the divergent developmental pathways observed in monocotyledonous versus dicotyledonous species. The PO and its annotation database (http://www.planteome.org) make plant data for any species more discoverable and accessible through common formats, thus providing support for applications in plant pathology, image analysis, and comparative development and evolution.
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