Summary
The Plant Structure Ontology (PSO) is a controlled vocabulary of anatomy and morphology of a generic flowering plant, developed by the Plant Ontology Consortium (POC) The main goal of the POC was to reduce the problem of heterogeneity of terminology used to describe comparable object types in plant genomic databases. PSO provides standardized set of terms describing anatomical and morphological structures pertinent to flowering plants during their normal course of development. Created as a tool for annotation of gene expression patterns and description of phenotypes across angiosperms, PSO is intended for plant genomics databases and broad plant genomic research community. Currently, this ontology encompasses diverse angiosperm taxa; further development will include new model organisms and important crop species. This chapter describes the rationales for creating PSO and discusses the guiding principles for its development and maintenance. The content of the PSO and the ontology browsing functionalities are outlined. The PSO can be browsed and downloaded at www.plantontology.org.
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Preview
Unable to display preview. Download preview PDF.
Similar content being viewed by others
References
J. Bard. Ontologies: formalizing biological knowledge for bioinformatics. BioEssays,25:501–506, 2003.
J.B. Bard, S.Y. Rhee, and M. Ashburner. An ontology for cell types. Genome Biology,6(R21), 2005.
T.Z. Berardini, S. Mundodi, L. Reiser, E. Huala, M. Garcia-Hernandez, P. Zhang, L.A.Mueller, J. Yoon, A. Doyle, G. Lander, N. Moseyko, D. Yoo, I. Xu, B. Zoeckler, M. Montoya,N. Miller, D. Weems, and SY. Rhee. Functional annotation of the Arabidopsisgenome using controlled vocabularies. Plant Physiol, 135:1–11, 2004.
A. Burger, D. Davidson, and R. Baldock. Formalization of mouse embryo anatomy. Bioinformatics,20:259–67, 2004.
J.I. Clark, C. Brooksbank, and J. Lomax. It’s all GO for plant scientists. Plant Physiol,138:1268–1278, 2005.
D. J. Craigon, N. James, J. Okyere, J. Higgins, J. Jotham, and S. May. NASCArrays:a repository for microarray data generated by NASC’s transcriptomics service. Nucleic Acids Res, 32:D575–7, 2004.
K. Esau. Anatomy of Seed Plants. Wiley & Sons, Inc., 2nd edition, 1977.
FlyBase Consortium. The FlyBase database of the Drosophila genome projects andcommunity literature. Nucleic Acids Res, 30:106–8, 2002.
Gene Ontology Consortium. Gene Ontology: tool for the unification of biology. Nature Genetics, 25:25–29, 2000.
Gene Ontology Consortium. Creating the gene ontology resource: design and implementation.Genome Res, 11:1425–1433, 2001.
T.F. Hayamizu, M. Mangan, J.P. Corradi, J.A. Kadin, andM. Ringwald. The Adult MouseAnatomical Dictionary: a tool for annotating and integrating data. Genome Biol, 6(R29),2005.
A. Hunter, M.H. Kaufman, A. McKay, R. Baldock, M.W. Simmen, and J.B. Bard. Anontology of human developmental anatomy. J Anat, 203:347–55, 2003.
K. Ilic, E.A. Kellogg, P. Jaiswal, F. Zapata, P.F. Stevens, L. Vincent, S. Avraham,L. Reiser, A. Pujar, M.M. Sachs, N.T. Whitman, S. McCouch, M. Schaeffer, D.H. Ware,L. Stein, and S.Y Rhee. The plant structure ontology - a unified vocabulary of anatomyand morphology of a flowering plant. Plant Physiology, 143:587–599, 2007.
P. Jaiswal, S. Avraham, K. Ilic, E.A. Kellogg, S. McCouch, A. Pujar, L. Reiser, S.Y. Rhee,M.M. Sachs, M. Schaeffer, L. Stein, P. Stevens, L. Vincent, D.Ware, and F. Zapata. PlantOntology (PO): A controlled vocabulary of plant structures and growth stages. Comp Funct Genom, 6:388–397, 2005.
P. Jaiswal, J. Ni, I. Yap, D. Ware, W. Spooner, K. Youens-Clark, L. Ren, C. Liang,W. Zhao, K. Ratnapu, B. Faga, P. Canaran, M. Fogleman, C. Hebbard, S. Avraham,S. Schmidt, T. M. Casstevens, E.S. Buckler, L. Stein, and S. McCouch. Gramene: abird’s eye view of cereal genomes. Nucleic Acids Res, 34:D717–23, 2006.
C.J. Lawrence, Q. Dong, M.L. Polacco, T.E. Seigfried, and V. Brendel. MaizeGDB, thecommunity database for maize genetics and genomics. Nucleic Acids Res, 32:D393–397,2004.
C. Mungall. Obol: Integrating language and meaning in bio-ontologies. Comp Funct Genom, 5:509–520, 2004.
Plant Ontology Consortium. The Plant Ontology Consortium and Plant Ontologies.Comp Funct Genom, 3:137–142, 2002.
A. Pujar, P. Jaiswal, E.A. Kellogg, K. Ilic, L. Vincent, S. Avraham, P. Stevens, F. Zapata,L. Reiser, S.Y. Rhee, M.M. Sachs, M. Schaeffer, L. Stein, D. Ware, and S. McCouch.Whole plant growth stage ontology for angiosperms and its application in plant biology.Plant Physiol, 142:414–428, 2006.
S.Y. Rhee, W. Beavis, T.Z. Berardini, G. Chen, D. Dixon, A. Doyle, M. Garcia-Hernandez, E. Huala, G. Lander, M. Montoya, N. Miller, L.A. Mueller, S. Mundodi,L. Reiser, J. Tacklind, D.C.Weems, Y.Wu, I. Xu, D. Yoo, J. Yoon, and P. Zhang. The ArabidopsisInformation Resource (TAIR): a model organism database providing a centralized,curated gateway to Arabidopsisbiology, research materials and community. Nucleic Acids Res, 31:224–228, 2003.
C. Rosse, A. Kumar, J.L. Mejino(Jr), D.L. Cook, L.T. Detwiler, and B. Smith. A strategyfor improving and integrating biomedical ontologies. In AMIA Annu Symp Proc., pages639–643, 2005.
B. Smith, W. Ceusters, B. Klagges, J. Kohler, A. Kumar, J. Lomax, C. Mungall,F. Neuhaus, A.L. Rector, and C. Rosse. Relations in biomedical ontologies. Genome Biol, 6(R46), 2005.
B. Smith, J. Williams, and S. Schulze-Kremer. The ontology of the gene ontology. InAMIA Annu Symp Proc, pages 609–613, 2003.
J. Sprague, L. Bayraktaroglu, D. Clements, T. Conlin, D. Fashena, K. Frazer, M. Haendel,D.G. Howe, P. Mani, S. Ramachandran, K. Schaper, E. Segerdell, P. Song, B. Sprunger,S. Taylor, C.E. Van Slyke, and M. Westerfield. The Zebrafish Information Network: thezebrafish model organism database. Nucleic Acids Res., 34:D581–5, 2006.
P.L. Vincent, E.H. Coe, and M.L. Polacco. Zea maysontology - a database of internationalterms. Trends in Plant Sci, 8:517–520, 2003.
Y. Yamazaki and P. Jaiswal. Biological ontologies in rice databases. an introduction tothe activities in Gramene and Oryzabase. Plant Cell Physiol, 46:63–68, 2005.
P. Zimmermann, M. Hirsch-Hoffmann, L. Hennig, and W. Gruissem. GENEVESTIGATOR.Arabidopsismicroarray database and analysis toolbox. Plant Physiol, 136:2621–32, 2004.
Editor information
Rights and permissions
Copyright information
© 2008 Albert Burger, Duncan Davidson, Richard Baldock
About this chapter
Cite this chapter
Ilic, K., Rhee, S.Y., Kellogg, E.A., Stevens, P.F. (2008). Plant Structure Ontology (PSO)— A Morphological and Anatomical Ontology of Flowering Plants. In: Burger, A., Davidson, D., Baldock, R. (eds) Anatomy Ontologies for Bioinformatics. Computational Biology, vol 6. Springer, London. https://doi.org/10.1007/978-1-84628-885-2_2
Download citation
DOI: https://doi.org/10.1007/978-1-84628-885-2_2
Publisher Name: Springer, London
Print ISBN: 978-1-84628-884-5
Online ISBN: 978-1-84628-885-2
eBook Packages: Computer ScienceComputer Science (R0)