Related Publications
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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
- Lens et al. 2012. An extension of the Plant Ontology project supporting wood anatomy and development research. IAWA Journal 33: 113–117.
- Walls et al (2012). A plant disease extension of the Infectious Disease Ontology. In Proceedings 3rd International Conference on Biomedical Ontology, Medical University of Graz, Graz, Austria.
- 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).
2008
- 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
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]
- 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
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.
- 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
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 OntologyTM 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]