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UniProt in RDF: Tackling Data Integration and Distributed Annotation with the Semantic Web

Nicole Redaschi¹ and UniProt Consortium²

Correspondence: (Login to view email address)

1. Swiss Institute of Bioinformatics (SIB)
2. Swiss Institute of Bioinformatics (SIB), European Bioinformatics Institute (EBI), Protein Information Resource (PIR)

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Document Type:

Poster

Date:

Received 28 April 2009 13:14 UTC; Posted 28 April 2009

Subjects:

Bioinformatics

Tags:

• Semantic Web
• Data integration
• Distributed annotation
• RDF
• uniprot
• UniProtKB
• biocuration

Abstract:

The UniProt knowledgebase (UniProtKB) is a comprehensive repository of protein sequence and annotation data. We collect information from the scientific literature and other databases and provide links to over one hundred biological resources. Such links between different databases are an important basis for data integration, but the lack of a common standard to represent and link information makes data integration an expensive business. At UniProt we have started to tackle this problem by using the Resource Description Framework (http://www.w3.org/RDF/) to represent our data. RDF is a core technology for the World Wide Web Consortium’s Semantic Web activities (http://www.w3.org/2001/sw/) and is therefore well suited to work in a distributed and decentralized environment. The RDF data model represents arbitrary information as a set of simple statements of the form subject-predicate-object. To enable the linking of data on the Web, RDF requires that each resource must have a (globally) unique identifier. These identifiers allow everybody to make statements about a given resource and, together with the simple structure of the RDF data model, make it easy to combine the statements made by different people (or databases) to allow queries across different datasets. RDF is thus an industry standard that can make a major contribution to solve two important problems of bioinformatics: distributed annotation and data integration.

Collection:

3rd International Biocuration Conference

Presented at:

3rd International Biocuration Conference, 16 April 2009

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License:

This document is licensed to the public under the Creative Commons Attribution 3.0 License

How to cite this document:

Redaschi, Nicole and Consortium, UniProt. UniProt in RDF: Tackling Data Integration and Distributed Annotation with the Semantic Web. Available from Nature Precedings <http://dx.doi.org/10.1038/npre.2009.3193.1> (2009)

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