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IBG-2 Seminar:
Dr. Ruth Bastow, University of Warwick, UK
Towards a Common Reference Ontology for Plants

06.12.2012 11:00 Uhr
Forschungszentrum Jülich, Gebäude 06.2 IBG-2, Seminarraum 406

Dr Bastow worked in several molecular biology labs focusing on Arabidopsis research including at the John Innes Centre, UK.

Since a few years, she coordinates GARNet, a BBSRC sponsored network to support plant research in Arabidopsis and other crops (

She has served as chair of the Multinational Arabidopsis Steering Committee. Her recent interests include the need of harmonizing and filling gaps in terminology used for phenotype and experiment annotation, and for plant experiment databases.

Towards a Common Reference Ontology for Plants

One of the central principles of biology is the concept that an organism’s genotype interacts with the environment to produce the observable characteristics, or phenotype. Understanding this interaction is a core goal of modern biology, and enables development of organisms with commercially useful characteristics through modern breeding programs.

Traditionally, phenotype information has been captured in a free text manner, which cannot be easily indexed and presents an obstacle to data sharing. Recent advances in next generation sequencing and phenotyping technologies have allowed researchers to access a growing mountain of data, resulting in an emerging gap between the genomics information and the quantitative information describing phenotypes and traits.

One way to bridge this gap is to use ontologies. Ontologies are a set of controlled vocabulary terms (e.g. seed, and endosperm) and relationships between those terms (e.g. endosperm is a part of a seed) that make biological statements accessible to computational approaches. The use of standardized, well-defined terms ensures that data generators, data managers and end users will use terms consistently, and defined relationships between terms ensure that computational reasoning can be applied to sets of data annotated using ontology terms.

There are numerous ontologies available for plant researchers and the presentation will look at some examples from the most utilized ontologies and assess how best to combine them in the future to create a semantic framework for meaningful cross-species queries using a Common Reference Ontology for Plants (cROP).

Contact: Dr. Fabio Fiorani