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 a variety of databases and instruments which are widespread by way of researchers within the biomedical box. notwithstanding, winning improvement of destiny bioinformatics functions depends upon an accurately formalised illustration of area knowledge.

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

Topics and Features:

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

• Considers a couple of primary modelling principles

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

• Explains contemporary 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 info at the Semantic Web

Although essentially written for readers who could be all for constructing the subsequent iteration of IT purposes within the parts of existence sciences, biomedical sciences and healthiness care, this particular quantity might be of curiosity to a person who will additional boost anatomy ontologies, who will use them, and who may be concerned with the particular improvement of proper (semantic) internet applications.

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Extra resources for Anatomy Ontologies for Bioinformatics: Principles and Practice

Example text

BioEssays, 25:501–506, 2003. 2. B. Y. Rhee, and M. Ashburner. An ontology for cell types. Genome Biology, 6(R21), 2005. 3. Z. Berardini, S. Mundodi, L. Reiser, E. Huala, M. Garcia-Hernandez, P. A. Mueller, J. Yoon, A. Doyle, G. Lander, N. Moseyko, D. Yoo, I. Xu, B. Zoeckler, M. Montoya, N. Miller, D. Weems, and SY. Rhee. Functional annotation of the Arabidopsis genome using controlled vocabularies. Plant Physiol, 135:1–11, 2004. 2 Plant Structure Ontology (PSO) 41 4. A. Burger, D. Davidson, and R.

Html). The DAG structure of the ontology allows a term to be placed in multiple branches of the ontology - a term can have multiple parents and consequently have relationships to more than one parental (higher-level) node [1]. Parent-child relationships are connecting links between the nodes in the ontological hierarchy. However, a general term cannot appear as a child of a more specific (lower level) term. This is because the relationships in the DAG structure are directional; no path 32 Katica Ilic, Seung Y.

Kellogg and Peter F. Stevens tists. The team that created PSO consisted of database curators and plant scientists, all experimental biologists by training. As expected, our main focus was the biological content of the ontology and the very pragmatic goal of providing a practical framework for annotations. The formal philosophical ontological rules and software implementations have been, to a large extent, neglected. The range of problems this approach created is similar to those described for some other informal bio-ontologies such as GO [23].

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