The Plant Ontology Database: a community resource for plant structure and developmental stages controlled vocabulary and annotations

The Plant Ontology Consortium (POC, http://www.plantontology.org) is a collaborative effort among model plant genome databases and plant researchers that aims to create, maintain and facilitate the use of a controlled vocabulary (ontology) for plants. The ontology allows users to ascribe attributes of plant structure (anatomy and morphology) and developmental stages to data types, such as genes and phenotypes, to provide a semantic framework to make meaningful cross-species and database comparisons. The POC builds upon groundbreaking work by the Gene Ontology Consortium (GOC) by adopting and extending the GOC's principles, existing software and database structure. Over the past year, POC has added hundreds of ontology terms to associate with thousands of genes and gene products from Arabidopsis, rice and maize, which are available through a newly updated web-based browser (http://www.plantontology.org/amigo/go.cgi) for viewing, searching and querying. The Consortium has also implemented new functionalities to facilitate the application of PO in genomic research and updated the website to keep the contents current. In this report, we present a brief description of resources available from the website, changes to the interfaces, data updates, community activities and future enhancement.

• Publication year

  2008

• Venue

  Nucleic Acids Res.

• Publication date

  2008-01-01

• Fields of study

  Biology, Medicine, Computer Science, Environmental Science

• Identifiers
  DOI 10.1093/nar/gkm908PMID 18194960PMCID 2238838
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• Whole-Plant Growth Stage Ontology for Angiosperms and Its Application in Plant Biology1[OA]

  2006cited by this paper
• The Plant Structure Ontology, a Unified Vocabulary of Anatomy and Morphology of a Flowering Plant1[W][OA]

  2006cited by this paper
• Gramene: a bird's eye view of cereal genomes

  2005influential reference
• Oryzabase. An Integrated Biological and Genome Information Database for Rice1[OA]

  2005cited by this paper
• Plant Ontology (PO): a Controlled Vocabulary of Plant Structures and Growth Stages

  2005cited by this paper
• Biological ontologies in rice databases. An introduction to the activities in Gramene and Oryzabase.

  2005cited by this paper
• An ontology for cell types

  2005cited by this paper
• The SOL Genomics Network. A Comparative Resource for Solanaceae Biology and Beyond1

  2005cited by this paper
• The International Rice Information System. A Platform for Meta-Analysis of Rice Crop Data

  2005cited by this paper
• Functional Annotation of the Arabidopsis Genome Using Controlled Vocabularies1

  2004cited by this paper
• Gene Ontology Consortium: The Gene Ontology (GO) database and informatics resource

  2004cited by this paper
• Zea mays ontology--a database of international terms.

  2003influential reference

• PscOA: A Plant scRNA-seq Marker Gene Database for Enhanced Cellular Transcriptome Understanding.

  2025cites this paper
• Artificial Intelligence in Medicinal Herb Breeding

  2025cites this paper
• Towards an Ontology-Driven System For Building and Farming Greenhouses

  2024cites this paper
• Ontology-Based Approach for Modeling Plant Growth Experiments

  2024cites this paper
• Genetic basis of expression and splicing underlying spike architecture in wheat (Triticum aestivum L.)

  2023cites this paper
• Genotype and phenotype data standardization, utilization and integration in the big data era for agricultural sciences

  2023cites this paper
• Sainfoin (Onobrychis spp.) crop ontology: supporting germplasm characterization and international research collaborations

  2023cites this paper
• Wissenschaftliche Grundlagen zum Strategiediskurs für einen nachhaltigen Pflanzenbau

  2022cites this paper
• Towards Improved Visualization and Optimization of Aquaculture Production Process

  2022cites this paper
• Creating and maintaining a high-confidence microRNA repository for crop research: A brief review and re-examination of the current crop microRNA registries.

  2022cites this paper
• Variation in cytonuclear expression accommodation among allopolyploid plants

  2022cites this paper
• Histidine kinase inhibitors impair shoot regeneration in Arabidopsis thaliana via cytokinin signaling and SAM patterning determinants

  2022cites this paper
• KinMod database: a tool for investigating metabolic regulation

  2022cites this paper
• Sample Identifiers and Metadata to Support Data Management and Reuse in Multidisciplinary Ecosystem Sciences

  2021cites this paper
• Opportunities and limits of controlled-environment plant phenotyping for climate response traits

  2021cites this paper
• An Ontology-Driven Personalized Faceted Search for Exploring Knowledge Bases of Capsicum

  2021cites this paper
• Vision, challenges and opportunities for a Plant Cell Atlas

  2021cites this paper
• Crop Planning and Production Process Ontology (C3PO), a New Model to Assist Diversified Crop Production

  2021cites this paper
• PCMDB: a curated and comprehensive resource of plant cell markers

  2021cites this paper
• Towards a Standardization of Terminology of the Climbing Habit in Plants

  2020cites this paper
• Towards a Standardization of Terminology of the Climbing Habit in Plants

  2020cites this paper
• WTO, an ontology for wheat traits and phenotypes in scientific publications

  2020cites this paper
• Knowledge representation and data sharing to unlock crop variation for nutritional food security

  2020cites this paper
• Modeling Crop Genetic Resources Phenotyping Information Systems

  2019cites this paper
• Genomic technologies for Hevea breeding.

  2019cites this paper
• Trait ontology analysis based on association mapping studies bridges the gap between crop genomics and Phenomics

  2019cites this paper
• Advancement in Sustainable Agriculture: Computational and Bioinformatics Tools

  2019cites this paper
• FoodOn: a harmonized food ontology to increase global food traceability, quality control and data integration

  2018cites this paper
• Semi-automatic Extraction of Plants Morphological Characters from Taxonomic Descriptions Written in Spanish

  2018cites this paper
• Building an Ontology of Flora of Thailand for Developing Semantic Electronic Dictionary

  2018cites this paper
• Where to search top-K biomedical ontologies?

  2018cites this paper
• CottonFGD: an integrated functional genomics database for cotton

  2017cites this paper
• Lawrence Berkeley National Laboratory Recent Work Title The Planteome database : An integrated resource for reference ontologies , plant genomics and phenomics Permalink

  2017cites this paper
• Identifying novel fruit-related genes in Arabidopsis thaliana based on the random walk with restart algorithm

  2017cites this paper
• Refinements to Hevea rubber breeding

  2017cites this paper
• Annotation Extensions.

  2017cites this paper
• New extension software modules to enhance searching and display of transcriptome data in Tripal databases

  2017cites this paper
• Genomics and Molecular Breeding

  2017cites this paper
• SoyBase: A Comprehensive Database for Soybean Genetic and Genomic Data

  2017cites this paper
• The Plani Plant Animation Framework

  2017cites this paper
• The Planteome database: an integrated resource for reference ontologies, plant genomics and phenomics

  2017cites this paper
• The Planteome Project

  2016cites this paper
• The BioHub Knowledge Base: Ontology and Repository for Sustainable Biosourcing

  2016cites this paper
• OBO EDIT: A TOOL FOR CLASSIFING THE BIOLOGICAL DATA

  2016cites this paper
• The flora phenotype ontology (FLOPO): tool for integrating morphological traits and phenotypes of vascular plants

  2016cites this paper
• ECOFI: a new generic database to analyse complex agroecological experimentation

  2016cites this paper
• A Semantic model for building integrated Ontology databases

  2016cites this paper
• Breeding vis-à-vis Genomics of Tropical Tree Crops

  2016cites this paper
• expVIP: a Customizable RNA-seq Data Analysis and Visualization Platform1[OPEN]

  2016influential citation
• A Shortest-Path-Based Method for the Analysis and Prediction of Fruit-Related Genes in Arabidopsis thaliana

  2016cites this paper
• Evolutionary Rate Heterogeneity of Primary and Secondary Metabolic Pathway Genes in Arabidopsis thaliana

  2015cites this paper
• Vers un système intelligent de capitalisation de connaissances pour l'agriculture durable : construction d'ontologies agricoles par transformation de sources existantes

  2015cites this paper
• Large-Scale Evolutionary Analysis of Genes and Supergene Clusters from Terpenoid Modular Pathways Provides Insights into Metabolic Diversification in Flowering Plants

  2015cites this paper
• Root System Markup Language: Toward a Unified Root Architecture Description Language1[OPEN]

  2015cites this paper
• How? Why? What? Where? When? Who? Grounding Ontology in the Actions of a Situated Social Agent

  2015cites this paper
• An Ontology-Based GIS for Genomic Data Management of Rumen Microbes

  2015cites this paper
• LegumeIP 2.0—a platform for the study of gene function and genome evolution in legumes

  2015cites this paper
• A Journey Through a Leaf: Phenomics Analysis of Leaf Growth in Arabidopsis thaliana

  2015cites this paper
• Enabling comparisons of characters using an Xper2 based knowledge-base of fern morphology

  2014cites this paper
• Next-generation genebanking: plant genetic resources management and utilization in the sequencing era

  2014cites this paper
• Web Services for Things

  2014influential citation
• Next-generation genebanking: plant genetic resources management and utilization in the sequencing era

  2014cites this paper
• A framework for the creation and exploration of cross platform expression compendia ; Een raamwerk voor het creëren en exploreren van cross-platform expressiecompendia

  2014cites this paper
• Information Retrieval in Life Sciences: A Programmatic Survey

  2014cites this paper
• A method for increasing expressivity of Gene Ontology annotations using a compositional approach

  2014cites this paper
• MAGIC: access portal to a cross-platform gene expression compendium for maize

  2014cites this paper
• Plant systems biology: insights, advances and challenges

  2014cites this paper
• Jasmonate Signaling

  2013cites this paper
• Next-generation phenotyping: requirements and strategies for enhancing our understanding of genotype–phenotype relationships and its relevance to crop improvement

  2013cites this paper
• Flexible scientific data management for plant phenomics research

  2013influential citation
• Controlled vocabularies for plant anatomical parts optimized for use in data analysis tools and for cross-species studies

  2013influential citation
• Role of Bioinformatics as a Tool in Tomato Research

  2013cites this paper
• Plant Databases and Data Analysis Tools

  2013cites this paper
• MicroRNA or NMD: why have two RNA silencing systems?

  2013cites this paper
• A guide to CORNET for the construction of coexpression and protein-protein interaction networks.

  2013cites this paper
• CartograTree: connecting tree genomes, phenotypes and environment

  2013cites this paper
• Integrating data to acquire new knowledge: Three modes of integration in plant science.

  2013cites this paper
• Comparative analyses of stress-responsive genes in Arabidopsis thaliana: insight from genomic data mining, functional enrichment, pathway analysis and phenomics.

  2013cites this paper
• CluePedia Cytoscape plugin: pathway insights using integrated experimental and in silico data

  2013cites this paper
• Management and dissemination of MS proteomic data with PROTICdb: Example of a quantitative comparison between methods of protein extraction

  2013cites this paper
• Building and Querying Microbial Ontology

  2013influential citation
• Silicon Era of Carbon-Based Life: Application of Genomics and Bioinformatics in Crop Stress Research

  2013cites this paper
• Molecular Breeding molecular breeding (MB) Platforms molecular breeding (MB) platforms (MBP) in World Agriculture

  2013cites this paper
• Genome-Wide Binding Analysis of the Transcription Activator IDEAL PLANT ARCHITECTURE1 Reveals a Complex Network Regulating Rice Plant Architecture[W]

  2013cites this paper
• PREDICTING COMPLEX PHENOTYPE-GENOTYPE RELATIONSHIPS IN GRASSES: A SYSTEMS GENETICS APPROACH

  2013cites this paper
• An integrative, translational approach to understanding rare and orphan genetically based diseases

  2013cites this paper
• Diagnostics in Plant Breeding

  2013cites this paper
• The Tomato Genome Sequencing Project

  2013cites this paper
• Maximizing capture of gene co-expression relationships through pre-clustering of input expression samples: an Arabidopsis case study

  2013cites this paper
• PlantGSEA: a gene set enrichment analysis toolkit for plant community

  2013cites this paper
• A smart web service based on the context of things

  2012influential citation
• CharaParser for fine-grained semantic annotation of organism morphological descriptions

  2012cites this paper
• Ontologies as integrative tools for plant science.

  2012cites this paper
• PICARA, an Analytical Pipeline Providing Probabilistic Inference about A Priori Candidates Genes Underlying Genome-Wide Association QTL in Plants

  2012cites this paper
• The Hordeum Toolbox - The Barley CAP Genotype and Phenotype Resource

  2012cites this paper
• A pragmatic approach for sustainable development based on semantic web services

  2012cites this paper
• Technical appraisal of strategic approaches to large-scale germplasm evaluation

  2012cites this paper
• New trends in peptide-based anti-biofilm strategies: a review of recent achievements and bioinformatic approaches

  2012cites this paper
• The Plant Ontology as a Tool for Comparative Plant Anatomy and Genomic Analyses

  2012influential citation
• Genomic Databases for Crop Improvement

  2012cites this paper