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

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 are actually various databases and instruments which are commonplace via researchers within the biomedical box. in spite of the fact that, profitable improvement of destiny bioinformatics purposes depends on an effectively formalised illustration of area knowledge.

This publication offers a well timed and first-of-its-kind selection of contributed chapters on anatomy ontologies. it really is interdisciplinary in its process, bringing jointly appropriate services from computing and biomedical reports, and protecting 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 present computational instruments and applications

• Considers a few basic modelling principles

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

• Explains fresh efforts to improve a typical 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 may be fascinated by constructing the following new release of IT functions within the parts of existence sciences, biomedical sciences and overall healthiness care, this certain quantity should be of curiosity to an individual who will extra advance anatomy ontologies, who will use them, and who should be occupied with the particular improvement of suitable (semantic) internet applications.

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Additional info for Anatomy Ontologies for Bioinformatics: Principles and Practice

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Plant structure) as a tool for facilitating annotation of genes and germplasms in angiosperms. Therefore, PSO can be characterized as an annotation-centric controlled vocabulary. , very granular terms are generally excluded) but should be sufficient to make possible the description of tissue samples and experimental data, such as mRNA expression patterns, protein localization, description of mutant phenotypes and natural variants. PSO is not designed as a botanical glossary or as a vocabulary for taxonomy for use in taxonomic databases.

2a). , automated reasoning and error checking), each term in the ontology is required to have at least one parent with an is a relationship. This specifies that every term in PSO is at least a subclass of plant structure. Several terms with missing is a relationship were detected in PSO by using the software tool Obol [17], and we are currently trying to assign a parent with an is a relationship to every term that is missing such a relationship. The part of relationship represents a component or subset relationship.

In Proceedings of Pac Symp Biocomput. 2004, pages 178– 189, 2004. 7. J. Hendler, T. Berners-Lee, and E. Miller. Integrating applications of the semantic web. J. Inst. Elec. Eng. Jap, pages 676–680, 2002. 8. A. H. Kaufman, A. McKay, R. W. B. Bard. An ontology of human developmental anatomy. , 203:347–355, 2003. 9. H. 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.

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