Related Publications

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  • Lens et al. 2012. An extension of the Plant Ontology project supporting wood anatomy and development research. IAWA Journal 33: 113–117.
  • Arnaud, et al (2012). Towards a Reference Plant Trait Ontology for Modeling Knowledge of Plant Traits and Phenotypes. Proceedings of the International Conference on Knowledge Engineering and Ontology Development. Barcelona, Spain, pp 220–225
  • Walls et al (2012). Ontologies as integrative tools for plant science. American Journal of Botany 99: 1263 –1275 (special invited paper).


  • Ilic et al, 2008. Plant Structure Ontology (PSO) - A morphological and anatomical ontology of flowering plants. In Anatomy Ontologies for Bioinformatics, Springer, p 27-42. Book
  • Avraham et al, 2008.The Plant Ontology Database: a community resource for plant structure and development stages controlled vocabulary and annotations. Abstract Full Text]
    Nucleic Acid Research, 36(Database issue):D449-D454


  • The OBO Foundry: Coordinated Evolution of Ontologies to Support Biomedical Data Integration”, Nature Biotechnology,25 (11), November 2007, 1251 -1255. [Smith et al, 2007]
  • Ilic et al, 2007.The Plant Structure Ontology, a unified vocabulary of anatomy and morphology of a flowering plant. [Abstract] [Full Text]
    Plant Physiology, 2007, 143: 587-599


  • Ontologies for data and knowledge sharing in biology: plant ROS signaling as a case study. [Abstract] [Full Text]
    Bioessays, 2006, Vol28(2): 199-210.
  • Pujar et al, 2006.Whole-plant growth stage ontology for angiosperms and its application in plant biology. [Abstract] [Full Text]
    Plant Physiology, 2006, 142: 414-428


  • Relations in Biomedical Ontologies”, Genome Biology (2005), 6 (5), R46. [Smith etal, 2005]



  • Zea mays ontology – a database of international terms
    Trends in Plant Science, 2003, 8(11): 517-520 [Abstract]


  • Extension and Integration of the Gene Ontology (GO): Combining GO Vocabularies With External Vocabularies. [Abstract] [Full Text]
    Genome research 2002,12: 1982-1991.

*The Plant OntologyTM Consortium and Plant Ontologies [Abstract] [Full Text]
Comparative and Functional Genomics, 2002, Vol 3(2), 137-142.

  • Surrounding Space: On the Ontology of Organism-Environment Relations. Theory in Biosciences 120:2 (2002), 139–162 [Smith and Varzi, 2002]


2000 and Older

  • On the representation of gene function in genetic databases. by Michael Ashburner, ISMB 1998. [HTML]
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