By Jonathan Bard (auth.), Albert Burger BSc, MSc, PhD, Duncan Davidson BSc, PhD, Richard Baldock BSc, PhD (eds.)

Bioinformatics as a self-discipline has come of age, and there at the moment are a variety of databases and instruments which are generic by means of researchers within the biomedical box. even if, profitable improvement of destiny bioinformatics functions depends upon an competently formalised illustration of area knowledge.

This ebook offers a well timed and first-of-its-kind selection of contributed chapters on anatomy ontologies. it really is interdisciplinary in its procedure, bringing jointly appropriate services from computing and biomedical experiences, and protecting either theoretical and utilized points, with an emphasis on more moderen paintings suitable to the rising Semantic Web.

Topics and Features:

• presents a complete dialogue of the principles of anatomical ontologies and the state-of-the-art in present computational instruments and applications

• Considers a few primary modelling principles

• contains chapters approximately examine on algorithms to systematically align anatomy ontologies and to mine facts within the literature, utilizing anatomy terms

• Explains contemporary efforts to improve a typical anatomy reference ontology

• Discusses anatomy within the context of spatio-temporal biomedical atlases

• Describes structures and instruments for linking anatomy ontologies with one another and with different online assets, similar to the biomedical literature

• Highlights the demanding situations of facing anatomy-based details at the Semantic Web

Although essentially written for readers who could be focused on constructing the following new release of IT purposes within the parts of lifestyles sciences, biomedical sciences and health and wellbeing care, this specified quantity can be of curiosity to someone who will extra improve anatomy ontologies, who will use them, and who may be fascinated with the particular improvement of suitable (semantic) internet applications.

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Additional resources for Anatomy Ontologies for Bioinformatics: Principles and Practice

Sample text

Stevens of the root node, plant structure (PO:0009011). There are 384 (or 53%) leaf terms, also called terminal nodes (the most specific terms with no children terms below), and 342 (47%) interior nodes (terms with children). Currently, PSO also has 304 synonyms assigned to 149 terms. , from the root node to the leaf node in the path) is 15 nodes, while an average ontology depth is 5 nodes. More detailed analysis of the ontology structure is provided elsewhere [13]. org) and displaying ontologies and annotations (ontology browsing tool, AmiGO).

P. Jaiswal, S. Avraham, K. A. Kellogg, S. McCouch, A. Pujar, L. Y. M. Sachs, M. Schaeffer, L. 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.

G. Howe, P. Mani, S. Ramachandran, K. Schaper, E. Segerdell, P. Song, B. Sprunger, S. E. Van Slyke, and M. Westerfield. The Zebrafish Information Network: the zebrafish model organism database. , 34:D581–5, 2006. 25. L. H. L. Polacco. Zea mays ontology - a database of international terms. Trends in Plant Sci, 8:517–520, 2003. 26. Y. Yamazaki and P. Jaiswal. Biological ontologies in rice databases. an introduction to the activities in Gramene and Oryzabase. Plant Cell Physiol, 46:63–68, 2005. 27. P.

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