Summary
This chapter reviews how the richness of animal and fungal anatomy can be incorporated into formal ontologies so that knowledge of tissue organisation can be made accessible both to biologists and to other computational resources. The first part of the chapter focuses on the anatomical and bioinformatics principles behind making these ontologies and the problems that have to be solved before they can be made. The next section reviews the anatomical ontologies currently available for the main model animal and fungal organisms. The final section focuses on the current and future uses of these ontologies, together with the problems of curating them and publishing up-to-date versions. The chapter ends with a plea for more and better software to make anatomical ontologies more accessible to the general biological community and so more useful to it.
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References
J.B.L. Bard. Anatomics: the intersection of anatomy and bioinformatics. J. Anatomy,206:1–16, 2005.
J.B.L. Bard and S.Y. Rhee. Ontologies in biology: design, applications, and future challenges.Nature Rev. Gen., 5:213–222, 2004.
M. Bownes. A photographic study of development in the living embryo of drosophila melanogaster. J Embryol Exp Morphol., 33:789–801, 1975.
A. Burger, D. Davidson, and R. Baldock. Formalization of mouse embryo anatomy. Bioinformatics,20:259–267, 2004.
D. Davidson and R. Baldock. Bioinformatics beyond sequence: mapping gene function in the embryo. Nat.Rev. Gen., 2:409–418, 2001.
G.V. Gkoutos, E.C. Green, A.M. Mallon, J.M. Hancock, and D. Davidson. Building mouse phenotype ontologies. In Proceedings of Pac Symp Biocomput. 2004, pages 178–189, 2004.
J. Hendler, T. Berners-Lee, and E. Miller. Integrating applications of the semantic web.J. Inst. Elec. Eng. Jap, pages 676–680, 2002.
A. Hunter, M.H. Kaufman, A. McKay, R. Baldock, M.W. Simmen, and J.B. Bard. An ontology of human developmental anatomy. J Anat., 203:347–355, 2003.
H. Parkinson. et al. The SOFG Anatomy Entry List (SAEL): an annotation tool for functional genomics data. Comp. Func. Genom., 5:521–527, 2004.
C. Rosse and J.L. Jr. Mejino. A reference ontology for biomedical informatics: the foundational model of anatomy. J Biomed Inform., 36:478–500, 2003.
P. Simons. Parts: a study in ontology. Oxford University Press, Oxford, UK, 1987.
B. Smith. Mereotopology: A theory of parts and boundaries. Data and Knowledge Engineering,20:287–303, 1996.
M.E. Winston, R. Chaffin, and D. Herrmann. A taxonomy of part-whole relations. Cognitive Science, 11:417–444, 1987.
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© 2008 Albert Burger, Duncan Davidson, Richard Baldock
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Bard, J. (2008). Anatomical Ontologies for Model Organisms: The Fungi and Animals. 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_1
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DOI: https://doi.org/10.1007/978-1-84628-885-2_1
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