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Ontologies as integrative tools for plant science.

TitleOntologies as integrative tools for plant science.
Publication TypeJournal Article
Year of Publication2012
AuthorsWalls, RL, Athreya B, Cooper L, Elser J, Gandolfo MA, Jaiswal P, Mungall CJ, Preece J, Rensing S, Smith B, Stevenson DW
JournalAmerican journal of botany
Volume99
Issue8
Start Page1
Pagination1-13
Date Published2012 Jul 30
ISSN1537-2197
Keywordsbio-ontologies; genome annotation; OBO Foundry; phenomics; plant anatomy; plant genomics; Plant Ontology; plant systematics; semantic web.
Abstract

• Premise of the study: Bio-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.

• Methods: This 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 results: Ontologies 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.

• Conclusions: Bio-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.

URLhttp://www.amjbot.org/content/early/2012/07/29/ajb.1200222.abstract
DOI10.3732/ajb.1200222
Refereed DesignationRefereed