The Plant Ontology as a Tool for Comparative Plant Anatomy and Genomic Analyses

By L. Cooper, R. Walls, James J. Elser, M. Gandolfo, Dennis W. Stevenson, Barry Smith, Justin Preece, Balaji Athreya, C. Mungall, S. Rensing and 12 more. 2012

193 citations recorded by the source corpus.

The Plant Ontology (PO; http://www.plantontology.org/) is a publicly available, collaborative effort to develop and maintain a controlled, structured vocabulary (‘ontology’) of terms to describe plant anatomy, morphology and the stages of plant development. The goals of the PO are to link (annotate) gene expression and phenotype data to plant structures and stages of plant development, using the data model adopted by the Gene Ontology. From its original design covering only rice, maize and Arabidopsis, the scope of the PO has been expanded to include all green plants. The PO was the first multispecies anatomy ontology developed for the annotation of genes and phenotypes. Also, to our knowledge, it was one of the first biological ontologies that provides translations (via synonyms) in non-English languages such as Japanese and Spanish. As of Release #18 (July 2012), there are about 2.2 million annotations linking PO terms to >110,000 unique data objects representing genes or gene models, proteins, RNAs, germplasm and quantitative trait loci (QTLs) from 22 plant species. In this paper, we focus on the plant anatomical entity branch of the PO, describing the organizing principles, resources available to users and examples of how the PO is integrated into other plant genomics databases and web portals. We also provide two examples of comparative analyses, demonstrating how the ontology structure and PO-annotated data can be used to discover the patterns of expression of the LEAFY (LFY) and terpene synthase (TPS) gene homologs.

Subfields: Molecular Biology

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Molecular Biology

Citations in the corpus

The Gene Ontology Resource: 20 years and still GOing strong (2018, background): “GO imports subsets of these external ontologies that include information about anatomical structures, cell types, chemicals and taxonomic groupings: Uberon (14), Protein Ontology (15), Plant Ontology (16) (23) and MetaCyc (24).”
Finding Our Way through Phenotypes (2015, background): “In a semantic graph, free text descriptions are converted into phenotype statements involving an anatomy term from animal or plant ontologies [56,118] and a quality term from a quality ontology [106], connected by a logical expression (‘‘inheres_in some’’).”
The Arabidopsis Information Resource: Making and Mining the ‘Gold Standard’ Annotated Reference Plant Genome (2015, methodology): “As with the GO annotations, the PO annotations facilitate cross experiment and cross species comparisons (Cooper et al ., 2013).”
The Cell Ontology 2016: enhanced content, modularization, and ontology interoperability (2016, background): “The Plant Ontology (PO) has recently undergone new developments and the PO team has taken responsibility for curation of all plant cell type classes [30].”
Gene Ontology Consortium: going forward (2014, background): “…(or stage) ontology (7), the Chemical Entities of Biological Inter-est ontology (ChEBI; (8)), the Plant Ontology for plant structure / stage (PO; (9)), the Phenotypic Quality Ontology (PATO; (10)) and the Sequence Ontology (SO; (11)), is called go-plus and is available at…”
Maize Metabolic Network Construction and Transcriptome Analysis (2013, background): “, 2012) by curating the appropriate plant anatomical entity (Ilic et al., 2007; Cooper et al., 2012) and the respective plant growth and development stage (Pujar et al.”
MetaboLights: a resource evolving in response to the needs of its scientific community (2019, background): “Plant Ontology (PO) (10), Units Ontology (UO) (11) Instrumentation MSIO (Metabolomics Standards Initiative Ontology), Chemical Methods Ontology (CHMO) (https://github.”