title: Controlled vocabularies for plant anatomical parts optimized for use in data analysis tools and for cross-species studies.
abstract: 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.
authors: Department of Biology, ETH Zurich, Zurich 8092, Switzerland. phz@nebion.com.
authors: Rasa
authors: R
authors: Meskauskiene
authors: Oliver
authors: O
authors: Laule
authors: Nikolai V
authors: NV
authors: Ivanov
authors: Florian
authors: F
authors: Martin
authors: Markus
authors: M
authors: Wyss
authors: Wilhelm
authors: W
authors: Gruissem
authors: Philip
authors: P
authors: Zimmermann
references: Nucleic Acids Res. 2008 Jan;36(Database issue):D947-53
references: 17984077
references: Plant Physiol. 2007 Feb;143(2):587-99
references: 17142475
references: Curr Opin Plant Biol. 1998 Feb;1(1):60-7
references: 10066562
references: Database (Oxford). 2011 May 29;2011:bar022
references: 21624896
references: BMC Genomics. 2012 Nov 28;13:674
references: 23190529
references: Nucleic Acids Res. 2012 Jan;40(Database issue):D1202-10
references: 22140109
references: Plant Cell Physiol. 2013 Feb;54(2):e1
references: 23220694
references: Trends Plant Sci. 2000 Feb;5(2):61-6
references: 10664615
references: Mol Plant. 2008 Sep;1(5):851-7
references: 19825587
references: Plant Cell Physiol. 2005 Jan;46(1):23-47
references: 15659435
references: Trends Plant Sci. 2004 Jan;9(1):42-8
references: 14729218
references: Nucleic Acids Res. 2008 Jan;36(Database issue):D449-54
references: 18194960