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

Abstract

AbstractThe 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/":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/":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.