Anatomy Ontologies for Bioinformatics: Principles and by Jonathan Bard (auth.), Albert Burger BSc, MSc, PhD, Duncan

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 quite a few databases and instruments which are widespread through researchers within the biomedical box. besides the fact that, profitable improvement of destiny bioinformatics functions relies on an accurately formalised illustration of area knowledge.

This publication presents a well timed and first-of-its-kind choice of contributed chapters on anatomy ontologies. it really is interdisciplinary in its technique, bringing jointly proper services from computing and biomedical stories, and masking either theoretical and utilized features, with an emphasis on more moderen paintings correct to the rising Semantic Web.

Topics and Features:

• presents a accomplished dialogue of the rules of anatomical ontologies and the cutting-edge in present computational instruments and applications

• Considers a couple of primary modelling principles

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

• Explains contemporary efforts to strengthen 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, reminiscent of the biomedical literature

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

Although essentially written for readers who may be curious about constructing the following iteration of IT functions within the parts of lifestyles sciences, biomedical sciences and healthiness care, this distinctive quantity may be of curiosity to someone who will extra improve anatomy ontologies, who will use them, and who may be serious about the particular improvement of correct (semantic) internet applications.

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Additional resources for Anatomy Ontologies for Bioinformatics: Principles and Practice

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3. a. A screenshot of the ontology browser - top nodes of the PSO. Clicking on the [+] or [–] sign in front of a term vertically expands or collapses the ontology tree, respectively. b. Expanded sporophyte node is indicated by curly bracket. A mouse click on a term itself opens a term detail page (see Fig. 1). Numbers in parentheses next to the term name indicate the number of the annotations for unique object types associated to a term (including annotations to all children terms). Relationship type icons are shown at the bottom right.

To search the PSO, the left-hand panel on the browser offers a choice of searching for terms (and synonyms) or gene symbols. When searching for terms in the PSO, users are advised to apply the Ontology filter, choosing the Plant Structure aspect; otherwise the search result page contains hits to both aspects of the Plant Ontology, the Plant Structure (PSO) and Plant Growth and Developmental Stages. For example, a search with the term mesophyll (not shown) resulted in 9 terms in the PSO that contained word mesophyll in a term name or in a synonym, including the term leaf mesophyll.

A photographic study of development in the living embryo of drosophila melanogaster. , 33:789–801, 1975. 4. A. Burger, D. Davidson, and R. Baldock. Formalization of mouse embryo anatomy. Bioinformatics, 20:259–267, 2004. 5. D. Davidson and R. Baldock. Bioinformatics beyond sequence: mapping gene function in the embryo. Rev. , 2:409–418, 2001. 6. V. C. M. M. Hancock, and D. Davidson. Building mouse phenotype ontologies. In Proceedings of Pac Symp Biocomput. 2004, pages 178– 189, 2004. 7. J. Hendler, T.

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