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Data integration gets 'Sloppy'

Nature Biotechnology volume 24, pages 1070–1071 (2006)Cite this article

To the editor:

Data integration in life sciences currently faces a conundrum1,2,3,4. On the one hand, the diversity of data is increasing as explosively as its volume. This makes it imperative that some degree of data formatting standardization is agreed upon by the diverse community generating and using that data. On the other hand, the value of individual data sets can only be appreciated when enough of those distinct pieces of the systemic puzzle are put together. Therefore, it is also imperative that standard formats not be enforced so strictly as to be an obstacle to reporting the very novel data that brings value to the targeted systemic integration. We present here a prototype application, termed Simple Sloppy Semantic Database (S3DB), that provides a bridge between loosely structured raw data annotated using personal ontologies and a globally referenceable semantic representation indexed to controlled vocabularies. Wide adoption of this database formalism has the potential to facilitate and optimize data management in a range of research fields, from molecular epidemiology to basic biology.

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Figure 1: Example of a S3DB application.

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Acknowledgements

This work was partially funded by the National Heart, Lung and Blood Institute of the US National Institutes of Health, under contract no. N01-HV-28181, and the PREVIS project (Pneumococcal Resistance Epidemicity and Virulence, An International Study), contract number LSHM-CT-2003-503413 from the European Commission.

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Authors and Affiliations

  1. Department of Biostatistics and Applied Mathematics, University of Texas, 1515 Holcombe Blvd., Box 0447, Houston, 77030-4009, Texas, USA

    Jonas S Almeida & Allen Chang

  2. Department of Biostatistics, Bioinformatics & Epidemiology, Medical University of South Carolina, 135 Cannon Street, Suite 303, Charleston, 29425, South Carolina, USA

    Chuming Chen, Robert Gorlitsky, Romesh Stanislaus & Xiaoshu Wang

  3. Instituto de Tecnologia Química e Biológica da Universidade Nova de Lisboa (ITQB/UNL), Av. da República (EAN), Oeiras, 2781-901, Portugal

    Jonas S Almeida, Marta Aires-de-Sousa, Pedro Eleutério, João Carriço, António Maretzek, Andreas Bohn & Helena F Deus

  4. Department of Molecular Therapeutics, Kleberg Center for Molecular Markers, University of Texas M. D. Anderson Cancer Center, 1515 Holcombe Blvd., Box 0317, Houston, 77030-4009, Texas, USA

    Fan Zhang, Rahul Mitra & Gordon B Mills

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  1. Jonas S Almeida
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  14. Xiaoshu Wang
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  15. Helena F Deus
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Almeida, J., Chen, C., Gorlitsky, R. et al. Data integration gets 'Sloppy'. Nat Biotechnol 24, 1070–1071 (2006). https://doi.org/10.1038/nbt0906-1070

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