The Plant Ontology: A Tool for Plant Genomics
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 wordsBioinformatics Ontology Plant anatomy Plant development Comparative genomics Genomeannotation Transcriptomics Phenomics Semantic web
The authors would like to acknowledge the contributions of the current and former members of the PO Project (http://plantontology.org/node/220) for their contributions to ontology development; the Gene Ontology Consortium (www.geneontology.org) for its leadership in the ontology field, for sharing software tools AmiGO an ontology browser, and the GO database package, which were both customized for the PO project; Christopher Sullivan (Center for Genome Research and Biocomputing at Oregon State University) for help with hosting and maintenance of the PO project web servers, and the members of the Jaiswal lab group at Oregon State University. We also acknowledge the iPlant Collaborative (http://www.iplantcollaborative.org/) for hosting a mirror site of PO (http://iplant.plantontology.org/). We extend special thanks to the numerous collaborators and domain experts (http://plantontology.org/node/8) who continue to contribute to the development and maintenance of the PO and the annotation database. This work was supported by the US National Science Foundation (Award # IOS:0822201 award).
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