TY - JOUR
KW - bio-ontologies; genome annotation; OBO Foundry; phenomics; plant anatomy; plant genomics; Plant Ontology; plant systematics; semantic web.
AU - Ramona Walls
AU - Balaji Athreya
AU - Laurel Cooper
AU - Justin Elser
AU - Maria Gandolfo
AU - Pankaj Jaiswal
AU - Christopher Mungall
AU - Justin Preece
AU - Stefan Rensing
AU - Barry Smith
AU - Dennis Stevenson
AB - • 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.
BT - American journal of botany
C1 - http://www.ncbi.nlm.nih.gov/pubmed/22847540?dopt=Abstract
DA - 2012 Jul 30
DO - 10.3732/ajb.1200222
IS - 8
LA - ENG
N2 - • 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.
PY - 2012
SE - 1
SP - 1
EP - 13
T2 - American journal of botany
TI - Ontologies as integrative tools for plant science.
UR - http://www.amjbot.org/content/early/2012/07/29/ajb.1200222.abstract
VL - 99
SN - 1537-2197
ER -