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This article is part of the supplement: Italian Society of Bioinformatics (BITS): Annual Meeting 2011

Open Access Research

Towards linked open gene mutations data

Achille Zappa12, Andrea Splendiani34 and Paolo Romano1*

Author Affiliations

1 Bioinformatics, IRCCS AOU San Martino-IST National Cancer Research Institute, Genoa, I-16132, Italy

2 Department of Informatics, Systems and Telematics, University of Genoa, Genoa, I-16145, Italy

3 Rothamsted Research, West Common, Harpenden, Hertfordshire, AL5 2JQ, UK

4 Digital Enterprise Research Institute, National University of Ireland at Galway, IDA Business Park, Lower Dangan, Galway, Ireland

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BMC Bioinformatics 2012, 13(Suppl 4):S7  doi:10.1186/1471-2105-13-S4-S7

Published: 28 March 2012

Abstract

Background

With the advent of high-throughput technologies, a great wealth of variation data is being produced. Such information may constitute the basis for correlation analyses between genotypes and phenotypes and, in the future, for personalized medicine. Several databases on gene variation exist, but this kind of information is still scarce in the Semantic Web framework.

In this paper, we discuss issues related to the integration of mutation data in the Linked Open Data infrastructure, part of the Semantic Web framework. We present the development of a mapping from the IARC TP53 Mutation database to RDF and the implementation of servers publishing this data.

Methods

A version of the IARC TP53 Mutation database implemented in a relational database was used as first test set. Automatic mappings to RDF were first created by using D2RQ and later manually refined by introducing concepts and properties from domain vocabularies and ontologies, as well as links to Linked Open Data implementations of various systems of biomedical interest.

Since D2RQ query performances are lower than those that can be achieved by using an RDF archive, generated data was also loaded into a dedicated system based on tools from the Jena software suite.

Results

We have implemented a D2RQ Server for TP53 mutation data, providing data on a subset of the IARC database, including gene variations, somatic mutations, and bibliographic references. The server allows to browse the RDF graph by using links both between classes and to external systems. An alternative interface offers improved performances for SPARQL queries. The resulting data can be explored by using any Semantic Web browser or application.

Conclusions

This has been the first case of a mutation database exposed as Linked Data. A revised version of our prototype, including further concepts and IARC TP53 Mutation database data sets, is under development.

The publication of variation information as Linked Data opens new perspectives: the exploitation of SPARQL searches on mutation data and other biological databases may support data retrieval which is presently not possible. Moreover, reasoning on integrated variation data may support discoveries towards personalized medicine.