ArticleAmerican journal of botany2012
Ontologies as integrative tools for plant science.
Article in American journal of botany, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 34 papers.
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Who cites it
34 citing papers in PubMed.
- Integrating cross-omics research through FAIR Digital Objects with DataPLANT.Journal of integrative bioinformatics · 2026Article
- Advancing utilization of diverse global carrot (Frontiers in plant science · 2024Article
- Evaluation of shoot-growth variation in diverse carrot (Frontiers in plant science · 2024Article
- TypeTaxonScript: sugarifying and enhancing data structures in biological systematics and biodiversity research.Biology methods & protocols · 2024Article
- WheatCENet: A Database for Comparative Co-expression Networks Analysis of Allohexaploid Wheat and Its Progenitors.Genomics, proteomics & bioinformatics · 2023Article
- Ontologies for increasing the FAIRness of plant research data.Frontiers in plant science · 2023Review
- DIVIS: a semantic DIstance to improve the VISualisation of heterogeneous phenotypic datasets.BioData mining · 2022Article
- RapGreen, an interactive software and web package to explore and analyze phylogenetic trees.NAR genomics and bioinformatics · 2021Article
- Challenges for FAIR-compliant description and comparison of crop phenotype data with standardized controlled vocabularies.Database : the journal of biological databases and curation · 2021Article
- The Ontologies Community of Practice: A CGIAR Initiative for Big Data in Agrifood Systems.Patterns (New York, N.Y.) · 2020Article
- Article
- Dealing with multi-source and multi-scale information in plant phenomics: the ontology-driven Phenotyping Hybrid Information System.The New phytologist · 2019Article
- The Plant Ontology Facilitates Comparisons of Plant Development Stages Across Species.Frontiers in plant science · 2019Article
- The anatomy of phenotype ontologies: principles, properties and applications.Briefings in bioinformatics · 2018Article
- Automated Integration of Trees and Traits: A Case Study Using Paired Fin Loss Across Teleost Fishes.Systematic biology · 2018Article
- QTLTableMinerBMC bioinformatics · 2018Article
- Bio-SimVerb and Bio-SimLex: wide-coverage evaluation sets of word similarity in biomedicine.BMC bioinformatics · 2018Article
- The Planteome database: an integrated resource for reference ontologies, plant genomics and phenomics.Nucleic acids research · 2018Article
- Plant data visualisation using network graphs.PeerJ · 2018Article
- DES-TOMATO: A Knowledge Exploration System Focused On Tomato Species.Scientific reports · 2017Article
Corrections and comments
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Authors and funding
11 authors.
Funding
Abstract
premise of the studyBio-ontologies are essential tools for accessing and analyzing the rapidly growing pool of plant genomic and phenomic data. Ontologies provide structured vocabularies to support consistent aggregation of data and a semantic framework for automated analyses and reasoning. They are a key component of the semantic web.
methodsThis paper provides background on what bio-ontologies are, why they are relevant to botany, and the principles of ontology development. It includes an overview of ontologies and related resources that are relevant to plant science, with a detailed description of the Plant Ontology (PO). We discuss the challenges of building an ontology that covers all green plants (Viridiplantae). KEY
resultsOntologies can advance plant science in four keys areas: (1) comparative genetics, genomics, phenomics, and development; (2) taxonomy and systematics; (3) semantic applications; and (4) education.
conclusionsBio-ontologies offer a flexible framework for comparative plant biology, based on common botanical understanding. As genomic and phenomic data become available for more species, we anticipate that the annotation of data with ontology terms will become less centralized, while at the same time, the need for cross-species queries will become more common, causing more researchers in plant science to turn to ontologies.
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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.