Ontology Resources

Internet resources and textbooks

• Angiosperm Phylogeny Web Glossary
• Esau K. 1977: Anatomy of Seed Plants, 2nd Edition. Wiley &Sons, Inc. ISBN:0471245208.
• Gifford E. M. and. Foster A. S, 1989. Morphology and evolution of vascular plants, 3rd Edition. W.H. Freeman & Co., New York. ISBN:0716719460.
• Kiesselbach, T. A. 1999: The Structure and Reproduction of Corn. 1999, 50th Anniversary Edition. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York. ISBN:0879695560.

List of projects working on ontologies

• Controlled Vocabulary and Ontologies for cereal plants (Gramene)
• Ontologies & Controlled Vocabularies for Gene Annotation of Arabidopsis (TAIR)
• Ontologies and Controlled Vocabularies for Maize (Maize Mapping Project)
• Ontologies to describe biochemical charateristics. Developed by Gene Ontology Consortium (GO)
• Open Biological Ontology Foundry: an open community for sharing ontologies (OBO)
• FAO's agricultural thesaurus (AGROVOC)
• Agricultural Ontology Service Project (AOS)

Publications

• 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.
  

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

• 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.

• 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.

• 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.

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

• 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]