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]