Get Anatomy Ontologies for Bioinformatics: Principles and PDF

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

ISBN-10: 1846288843

ISBN-13: 9781846288845

ISBN-10: 1846288851

ISBN-13: 9781846288852

Bioinformatics as a self-discipline has come of age, and there are actually quite a few databases and instruments which are primary via researchers within the biomedical box. besides the fact that, winning improvement of destiny bioinformatics purposes is dependent upon an accurately formalised illustration of area knowledge.

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

Topics and Features:

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

• Considers a few primary modelling principles

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

• Explains contemporary efforts to advance a standard anatomy reference ontology

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

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

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

Although essentially written for readers who can be keen on constructing the following new release of IT purposes within the parts of lifestyles sciences, biomedical sciences and healthiness care, this particular quantity could be of curiosity to an individual who will extra advance anatomy ontologies, who will use them, and who should be fascinated about the particular improvement of suitable (semantic) net applications.

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Extra resources for Anatomy Ontologies for Bioinformatics: Principles and Practice

Example text

For example, a user who is interested in all genes that have mutant phenotypes affecting embryo development and all genes that are expressed in the embryo, can search for the term embryo in the AmiGO browser and will quickly retrieve all gene annotations and phenotypic descriptions associated to this term (and its children terms) for Arabidopsis, rice and maize, as shown in Fig. 4. Hyperlinks to the individual databases that contributed the annotation provide a quick access to additional information about annotated genes and germplasms.

Avraham, P. Stevens, F. Zapata, L. Y. 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. 20. Y. Rhee, W. Z. Berardini, G. Chen, D. Dixon, A. Doyle, M. GarciaHernandez, E. Huala, G. Lander, M. Montoya, N. A. Mueller, S. Mundodi, L. Reiser, J. C. Weems, Y. Wu, I. Xu, D. Yoo, J. Yoon, and P. Zhang. The Arabidopsis Information Resource (TAIR): a model organism database providing a centralized, curated gateway to Arabidopsis biology, research materials and community.

Parkinson. et al. The SOFG Anatomy Entry List (SAEL): an annotation tool for functional genomics data. Comp. Func. , 5:521–527, 2004. 10. C. L. Jr. Mejino. A reference ontology for biomedical informatics: the foundational model of anatomy. , 36:478–500, 2003. 11. P. Simons. Parts: a study in ontology. Oxford University Press, Oxford, UK, 1987. 12. B. Smith. Mereotopology: A theory of parts and boundaries. Data and Knowledge Engineering, 20:287–303, 1996. 13. E. Winston, R. Chaffin, and D. Herrmann.

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

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