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This article is part of the supplement: Semantic Web Applications and Tools for Life Sciences (SWAT4LS), 2009

Open Access Highly Accessed Research

Linking the Resource Description Framework to cheminformatics and proteochemometrics

Egon L Willighagen*, Jonathan Alvarsson, Annsofie Andersson, Martin Eklund, Samuel Lampa, Maris Lapins, Ola Spjuth and Jarl ES Wikberg

Author Affiliations

Uppsala University, Department of Pharmaceutical Biosciences, Box 591, SE-751 24 Uppsala, Sweden

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Journal of Biomedical Semantics 2011, 2(Suppl 1):S6  doi:10.1186/2041-1480-2-S1-S6

Published: 7 March 2011

Abstract

Background

Semantic web technologies are finding their way into the life sciences. Ontologies and semantic markup have already been used for more than a decade in molecular sciences, but have not found widespread use yet. The semantic web technology Resource Description Framework (RDF) and related methods show to be sufficiently versatile to change that situation.

Results

The work presented here focuses on linking RDF approaches to existing molecular chemometrics fields, including cheminformatics, QSAR modeling and proteochemometrics. Applications are presented that link RDF technologies to methods from statistics and cheminformatics, including data aggregation, visualization, chemical identification, and property prediction. They demonstrate how this can be done using various existing RDF standards and cheminformatics libraries. For example, we show how IC50 and Ki values are modeled for a number of biological targets using data from the ChEMBL database.

Conclusions

We have shown that existing RDF standards can suitably be integrated into existing molecular chemometrics methods. Platforms that unite these technologies, like Bioclipse, makes this even simpler and more transparent. Being able to create and share workflows that integrate data aggregation and analysis (visual and statistical) is beneficial to interoperability and reproducibility. The current work shows that RDF approaches are sufficiently powerful to support molecular chemometrics workflows.