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.
Keywords: Semantic web, ontology, bio-ontology, PATO, XML, phenotype descriptions
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