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From XML to RDF: how semantic web technologies will change the design of 'omic' standards

Abstract

With the ongoing rapid increase in both volume and diversity of 'omic' data (genomics, transcriptomics, proteomics, and others), the development and adoption of data standards is of paramount importance to realize the promise of systems biology. A recent trend in data standard development has been to use extensible markup language (XML) as the preferred mechanism to define data representations. But as illustrated here with a few examples from proteomics data, the syntactic and document-centric XML cannot achieve the level of interoperability required by the highly dynamic and integrated bioinformatics applications. In the present article, we discuss why semantic web technologies, as recommended by the World Wide Web consortium (W3C), expand current data standard technology for biological data representation and management.

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Figure 1: A hypothetical 2DE example.
Figure 2: Data relationships for a spot on a 2DE gel and its XML representation.
Figure 3: Graph model for an RDF statement.
Figure 4: An RDF model for a spot on a 2DE gel.

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Acknowledgements

This work was supported by the US National Heart, Lung, and Blood Institute (NHLBI) Proteomics Initiative through contract N01-HV-28181 to the Medical University of South Carolina, Principal Investigator. D. Knapp, and its bioinformatics core (core C, Principal Investigator J.S. Almeida) and mathematical modeling project (project 7, Principal Investigator E.O. Voit), as well as by its administrative center, separately funded by the same initiative to the same institution, Principal Investigator M.P. Schachte. The authors also acknowledge support by the training grant 1-T15-LM07438-01 “training of toolmakers for Biomedical Informatics” by the US National Library of Medicine of the National Institutes of Health, (NIH/NLM).

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Correspondence to Jonas S Almeida.

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Wang, X., Gorlitsky, R. & Almeida, J. From XML to RDF: how semantic web technologies will change the design of 'omic' standards. Nat Biotechnol 23, 1099–1103 (2005). https://doi.org/10.1038/nbt1139

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