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 a number of databases and instruments which are customary by means of researchers within the biomedical box. although, winning improvement of destiny bioinformatics purposes relies on an correctly formalised illustration of area knowledge.

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

Topics and Features:

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

• Considers a couple of primary modelling principles

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

• Explains contemporary efforts to improve 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, 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 fascinated about constructing the following new release of IT functions within the components of lifestyles sciences, biomedical sciences and healthiness care, this certain quantity could be of curiosity to somebody who will additional advance anatomy ontologies, who will use them, and who should be considering the particular improvement of correct (semantic) net applications.

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Extra resources for Anatomy Ontologies for Bioinformatics: Principles and Practice

Example text

They are poor at illustrating knowledge (only OBOedit currently provides any graphical visualisation beyond the basic hierarchy), partly because there can be so much material that a screenshot gives too little of the whole, and partly because the ontologies can be so rich that their visualisation is too complex to allow a user to look at the implications of a single relationship in a multirelationship ontology. They are thus not necessarily helpful to someone who wishes to use the ontology as a knowledge resource.

In practice, this has meant that ontologies may need to be available in different formats and in restricted forms. The deeper truth here is that ontologies are made for specific purposes and it may be best to view that which holds the most tissues and richest relationships as the standard but that subontolgoies should be available as required. The net result is that anatomical ontologies may need to be released in several formats and to be upgraded as new knowledge is incorporated and corrections made.

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. Clicking on the tree icon right below the check box in the first column, multiple term lineages for the leaf mesophyll in the PSO will be displayed. This term is placed under tissue (as a type of a parenchyma tissue), and also under organ and sporophyte nodes (as a part of a leaf). Children terms of the term leaf mesophyll can be viewed by expanding the ontology tree downward, after clicking on the [+] sign in front of the term accession (PO:0005645).

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