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Ontologies as integrative tools for plant science
Author(s) -
Walls Ramona L.,
Athreya Balaji,
Cooper Laurel,
Elser Justin,
Gandolfo Maria A.,
Jaiswal Pankaj,
Mungall Christopher J.,
Preece Justin,
Rensing Stefan,
Smith Barry,
Stevenson Dennis W.
Publication year - 2012
Publication title -
american journal of botany
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.218
H-Index - 151
eISSN - 1537-2197
pISSN - 0002-9122
DOI - 10.3732/ajb.1200222
Subject(s) - ontology , phenomics , open biomedical ontologies , computer science , semantic web , data science , ontology components , idef5 , biology , genomics , process ontology , world wide web , ontology alignment , genome , philosophy , biochemistry , epistemology , gene
• 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.