Plant Bioinformatics

Volume 1374 of the series Methods in Molecular Biology pp 89-114

The Plant Ontology: A Tool for Plant Genomics

  • Laurel CooperAffiliated withDepartment of Botany and Plant Pathology, Oregon State University
  • , Pankaj JaiswalAffiliated withDepartment of Botany and Plant Pathology, Oregon State University Email author 

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The use of controlled, structured vocabularies (ontologies) has become a critical tool for scientists in the post-genomic era of massive datasets. Adoption and integration of common vocabularies and annotation practices enables cross-species comparative analyses and increases data sharing and reusability. The Plant Ontology (PO; http://​www.​plantontology.​org/​) describes plant anatomy, morphology, and the stages of plant development, and offers a database of plant genomics annotations associated to the PO terms. The scope of the PO has grown from its original design covering only rice, maize, and Arabidopsis, and now includes terms to describe all green plants from angiosperms to green algae.

This chapter introduces how the PO and other related ontologies are constructed and organized, including languages and software used for ontology development, and provides an overview of the key features. Detailed instructions illustrate how to search and browse the PO database and access the associated annotation data. Users are encouraged to provide input on the ontology through the online term request form and contribute datasets for integration in the PO database.

Key words

Bioinformatics Ontology Plant anatomy Plant development Comparative genomic s Genome annotation Transcriptomics Phenomics Semantic web