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 are actually a number of databases and instruments which are customary via researchers within the biomedical box. despite the fact that, profitable improvement of destiny bioinformatics functions depends on an effectively formalised illustration of area knowledge.

This booklet presents a well timed and first-of-its-kind choice of contributed chapters on anatomy ontologies. it truly is interdisciplinary in its technique, bringing jointly proper services from computing and biomedical reports, and overlaying either theoretical and utilized elements, with an emphasis on more recent paintings proper to the rising Semantic Web.

Topics and Features:

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

• Considers a couple of primary modelling principles

• comprises chapters approximately study on algorithms to systematically align anatomy ontologies and to mine information 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 structures and instruments for linking anatomy ontologies with one another and with different online assets, equivalent to the biomedical literature

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

Although basically written for readers who could be concerned about constructing the subsequent new release of IT functions within the parts of lifestyles sciences, biomedical sciences and overall healthiness care, this precise quantity may be of curiosity to an individual who will additional increase anatomy ontologies, who will use them, and who could be desirous about the particular improvement of proper (semantic) internet applications.

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Extra resources for Anatomy Ontologies for Bioinformatics: Principles and Practice

Sample text

There are a number of problems where there is no consensus on solutions. Of particular importance are the relations of tissues and substances to structures and representation of characteristics collective effects of entities such as cells, One approach to this issue is discussed here. Finally, there is currently no expressively adequate and computationally tractable means for expressing abnormal and variant anatomy. All resources are explicitly about ”normative anatomy”. e. the labeling of entities from their formal definitions and relations.

2). A similar abstract format is available for the zebrafish anatomy. The ontology of mouse adult anatomy includes multi-parent links and is thus a DAG. Human developmental anatomy for the Carnegie stages (up to E50 or so) is available as an ontology for annotation, albeit at a coarser granularity than the ontology for mouse developmental anatomy on which it is based. uk/anatomy/humat/) for consultation and this version gives the basic hierarchies with links to formal notes about the provenance of the data as well as further links to the literature [8].

Parkinson, personal communication). As of August 31, 2006, the POC database has over 4,400 unique object 38 Katica Ilic, Seung Y. Rhee, Elizabeth A. Kellogg and Peter F. Stevens Fig. 4. Ontology browser term detail view for the term embryo (PO:0009009), showing selected annotations for this term. 2 Plant Structure Ontology (PSO) 39 types (genes and germplasms) annotated with PSO terms amounting to over 10,000 annotations. These annotations were contributed by TAIR, Gramene, MaizeGDB and NASC. Functional annotation of genes and gene products can be described as a process of extracting information about gene function at the molecular level, its biological role(s), protein localization, and its spatial/temporal expression patterns during plant development [3].

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