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Towards a Phenotypic Semantic Web

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The impact of the internet in Biology is undeniable. The next stage in the evolution of the Internet for biological and molecular resource discovery must be towards what has been described as a semantic Web, where not only humans but machines can make "biologically intelligent" decisions based on collections of authenticable assertions about biology and molecular sciences. This vision requires agreed common representations of data and metadata shared and processed by automated tools as well as by people. Ontologies have become an integral part of achieving this and transformed biological resource management.

In this review, we describe the necessary transition steps from the initial conception of the internet to the realisation of the semantic web using as an example its application in phenotypic information construction and delivery. We review the different parts of the Semantic web, such as XML, metadata, RDF, OWL, digital signatures, ontologies and grids whilst concentrating on how ontology is applied in Biology and more specifically in phenotype annotation. Finally, we discuss how the semantic web will transform biological information management, retrieval and visualisation whilst ensuring the availability of high quality data of the correct type and format for the determination of model structures and biological systems.

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Keywords: PATO; Semantic web; XML; bio-ontology; ontology; phenotype descriptions

Document Type: Research Article

Affiliations: Department of Genetics, University of Cambridge, Downing Street, Cambridge, CB2 3EH, UK.

Publication date: 01 May 2006

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  • Current Bioinformatics aims to publish all the latest and outstanding developments in bioinformatics. Each issue contains a series of timely, in-depth reviews written by leaders in the field, covering a wide range of the integration of biology with computer and information science.

    The journal focuses on reviews on advances in computational molecular/structural biology, encompassing areas such as computing in biomedicine and genomics, computational proteomics and systems biology, and metabolic pathway engineering. Developments in these fields have direct implications on key issues related to health care, medicine, genetic disorders, development of agricultural products, renewable energy, environmental protection, etc.

    Current Bioinformatics is an essential journal for all academic and industrial researchers who want expert knowledge on all major advances in bioinformatics.
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