Controlled vocabularies for plant anatomical parts optimized for use in data analysis tools and for cross-species studies

Plant Methods

Philip Zimmermann²  Wilhelm Gruissem¹  Markus Wyss²  Florian Martin³  Nikolai V Ivanov³  Oliver Laule²  Rasa Meskauskiene² 

[1] Department of Biology, ETH Zurich, Zurich 8092, Switzerland;NEBION AG, Hohlstrasse 515, Zurich 8048, Switzerland;Philip Morris International R&D, Quai Jeanrenaud 5, Neuchatel 2003, Switzerland

关键词: Database;    Ontology;    Controlled vocabularies;    Plant anatomy;   

Others  :  812608
DOI  :  10.1186/1746-4811-9-33

 received in 2013-04-23, accepted in 2013-07-13,  发布年份 2013

【 摘 要 】

Background

It is generally accepted that controlled vocabularies are necessary to systematically integrate data from various sources. During the last decade, several plant ontologies have been developed, some of which are community specific or were developed for a particular purpose. In most cases, the practical application of these ontologies has been limited to systematically storing experimental data. Due to technical constraints, complex data structures and term redundancies, it has been difficult to apply them directly into analysis tools.

Results

Here, we describe a simplified and cross-species compatible set of controlled vocabularies for plant anatomy, focussing mainly on monocotypledonous and dicotyledonous crop and model plants. Their content was designed primarily for their direct use in graphical visualization tools. Specifically, we created annotation vocabularies that can be understood by non-specialists, are minimally redundant, simply structured, have low tree depth, and we tested them practically in the frame of Genevestigator.

Conclusions

The application of the proposed ontologies enabled the aggregation of data from hundreds of experiments to visualize gene expression across tissue types. It also facilitated the comparison of expression across species. The described controlled vocabularies are maintained by a dedicated curation team and are available upon request.

【 授权许可】

   
2013 Meskauskiene et al.; licensee BioMed Central Ltd.

【 图 表 】

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