02256nas a2200289   4500000000100000000000100001008004100002260001600043653014300059100001700202700001900219700001800238700001700256700001900273700001900292700002400311700001800335700001900353700001600372700002100388245005500409856007200464300000900536490000700545520140000552022001401952       2012                            d  c2012 Jul 3010abio-ontologies; genome annotation; OBO Foundry; phenomics; plant anatomy; plant genomics; Plant Ontology; plant systematics; semantic web.1 aRamona Walls1 aBalaji Athreya1 aLaurel Cooper1 aJustin Elser1 aMaria Gandolfo1 aPankaj Jaiswal1 aChristopher Mungall1 aJustin Preece1 aStefan Rensing1 aBarry Smith1 aDennis Stevenson00aOntologies as integrative tools for plant science.  uhttp://www.amjbot.org/content/early/2012/07/29/ajb.1200222.abstract  a1-130 v993 a• 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.  a1537-2197