Related Publications

2013

• Cooper and Walls et al (2013) The Plant Ontology as a Tool for Comparative Plant Anatomy and Genomic Analyses. Plant and Cell Physiology 54: e1–e1

2012

• Ontologies as integrative tools for plant science. American Journal of Botany 99: 1263 –1275 (special invited paper).

• A plant disease extension of the Infectious Disease Ontology. In Proceedings 3rd International Conference on Biomedical Ontology, Medical University of Graz, Graz, Austria.

• Lens, F., L. Cooper, M.A. Gandolfo, A. Groover, P. Jaiswal, B. Lachenbruch, R. Spicer, et al. 2012. An extension of the Plant Ontology project supporting wood anatomy and development research. IAWA Journal 33: 113–117.

• Arnaud E, Cooper L, Shrestha R, Menda N, Nelson RT, Matteis L, Skofic M, Bastow R, Jaiswal P, Mueller L, 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

2008

• Plant Structure Ontology (PSO) - A morphological and anatomical ontology of flowering plants. In Anatomy Ontologies for Bioinformatics, Springer, 2008, p 27-42. Book

• The Plant Ontology Database: a community resource for plant structure and development stages controlled vocabulary and annotations. Abstract Full Text]
  Nucleic Acid Research, 2008, 36(Database issue):D449-D454

2007

• The OBO Foundry: Coordinated Evolution of Ontologies to Support Biomedical Data Integration”, Nature Biotechnology,25 (11), November 2007, 1251 -1255. [Smith 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
  

2006

• Bioinformatics and its applications in plant biology. [Abstract] [Full Text]
  Annual Review of Plant Biology, 2006, Vol 57: 335-360.
  

• Ontologies for data and knowledge sharing in biology: plant ROS signaling as a case study. [Abstract] [Full Text]
  Bioessays, 2006, Vol28(2): 199-210.
  

• Whole-plant growth stage ontology for angiosperms and its application in plant biology. [Abstract] [Full Text]
  Plant Physiology, 2006, 142: 414-428

2005

• An ontology for cell types. [Abstract] [Full Text]
  Genome Biology, 2005, Vol 6: R21.
  

• Plant Ontology (PO): a controlled vocabulary of plant structures and growth stages. [Abstract] [Full Text]
  Comparative and Functional Genomics, 2005, Volume 6(7-8), 388 - 397

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

2004

• The Gene Ontology (GO) database and informatics resource. [Abstract] [Full Text]
  Nucleic Acids Research, 2004, Vol 32: D258-D261.

• Bio-ontologies-fast and furious. [Full Text]
  Nature Biotechnology, 2004, Vol 22(6): 773-774.

• Functional annotation of the Arabidopsis genome using controlled vocabularies. [Abstract] [Full Text]
  Plant Physiology, 2004, Vol 135(2): 745-755.

• Ontologies in biology: design, applications and future challenges. [Abstract] [Full Text]
  Nature Reviews Genetics 2004, Vol 5(3): 213-222.

2003

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

• Ontologies: Formalising biological knowledge for bioinformatics. [Abstract] [Full Text]
  Bioessays, 2003, Vol 25(5): 501-506.

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

2002

• 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 Ontology^TM Consortium and Plant Ontologies [Abstract] [Full Text]
Comparative and Functional Genomics, 2002, Vol 3(2), 137-142.

• Gramene: development and integration of trait and gene ontologies for rice [Abstract] [Full Text]
  Comparative and Functional Genomics, 2002, Vol 3(2), 132-136.

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

2001

• Creating the gene ontology resource: design and implementation. [Abstract] [Full Text]
  Genome Research, 2001, Vol 11(8), 1425-1433.

2000 and Older

• Gene Ontology: tool for the unification of biology. [Abstract] [Full Text]
  Nature Genetics, 2000, 25: 25-29.

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