By Albert Burger, Duncan Davidson, Richard Baldock
This publication presents a well timed and first-of-its-kind selection of papers on anatomy ontologies. it's interdisciplinary in its process, bringing jointly the appropriate services from computing and biomedical experiences. The publication goals to supply readers with a finished realizing of the rules of anatomical ontologies and the-state-of-the-art when it comes to present instruments and purposes. It additionally highlights demanding situations that stay this day.
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Extra info for Anatomy Ontologies for Bioinformatics: Principles and Practice (Computational Biology)
Rhee. Functional annotation of the Arabidopsis genome using controlled vocabularies. Plant Physiol, 135:1–11, 2004. 2 Plant Structure Ontology (PSO) 41 4. A. Burger, D. Davidson, and R. Baldock. Formalization of mouse embryo anatomy. Bioinformatics, 20:259–67, 2004. 5. I. Clark, C. Brooksbank, and J. Lomax. It’s all GO for plant scientists. Plant Physiol, 138:1268–1278, 2005. 6. 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.
Stein, P. Stevens, L. Vincent, D. Ware, and F. Zapata. Plant Ontology (PO): A controlled vocabulary of plant structures and growth stages. Comp Funct Genom, 6:388–397, 2005. 15. 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. S. Buckler, L. Stein, and S. McCouch. Gramene: a bird’s eye view of cereal genomes. Nucleic Acids Res, 34:D717–23, 2006. 16. J. Lawrence, Q. L.
Fruit ﬂy , mouse [4, 11], zebraﬁsh , and humans . Anatomical vocabularies were developed for a few plant species too, such as Arabidopsis , maize  and cereals . , Cereal Plant Anatomy Ontology). No attempts were made to map the existing plant ontologies to each other, conceivably due to apparent variation in nomenclature and different organizational principles on which these vocabularies were built. Following the GO paradigm and embracing the idea of a generic, standardized terminology that would ultimately encompass many ﬂowering plants, and that would allow for comparison across species, the Plant Ontology Consortium (POC) developed the ﬁrst controlled vocabulary of anatomy and morphology of ﬂowering plants, the Plant Structure Ontology (PSO) .
Anatomy Ontologies for Bioinformatics: Principles and Practice (Computational Biology) by Albert Burger, Duncan Davidson, Richard Baldock