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Discovering and linking public omics data sets using the Omics Discovery Index

Nature Biotechnology volume 35, pages 406–409 (2017)Cite this article

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To the Editor:

Biomedical data are being produced at an unprecedented rate owing to the falling cost of experiments and wider access to genomics, transcriptomics, proteomics and metabolomics platforms1,2. As a result, public deposition of omics data is on the increase. This presents new challenges, including finding ways to store, organize and access different types of biomedical data stored on different platforms. Here, we present the Omics Discovery Index (OmicsDI; http://www.omicsdi.org), an open-source platform that enables access, discovery and dissemination of omics data sets.

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Figure 1: Omics Discovery Index: data standardization, annotation, index and presentation.
Figure 2: Distributions of OmicsDI data sets.

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Acknowledgements

This work has been supported by the US NIH BD2K grant U54 GM114833 and a National Natural Science Foundation of China grant (61501071). A.I.N. is supported by US National Institute of Health grant (R01-GM-094231). Y.P.-R. is supported by BBSRC 'PROCESS' grant (BB/K01997X/1). M.B. is supported by Projects of International Cooperation and Exchanges grant (2014DFB30010). M.W. is supported by an NIH grant (5P41GM103484-07). J.A.V. and N.d.-T. are supported by the Wellcome Trust (grant WT101477MA). T.T. is supported by the BBSRC 'ProteoGenomics' grant (BB/L024225/1). E.W.D. and D.S.C. are supported in part by grant (U24 AI117966-02S1). S.-A.S. is supported in part by US NIH BD2K grant (1U24AI117966-01). M.W. and N.Bandeira were supported by NIH grant (5P41GM103484-07). N.Bandeira was also partially supported as an Alfred P. Sloan Fellow. S.Subramaniam is supported by NIH grants U01 DK097430 and U01 CA198941

Author information

Author notes

  1. Yasset Perez-Riverol and Mingze Bai: These authors contributed equally to this work.

Authors and Affiliations

  1. European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, United Kingdom

    Yasset Perez-Riverol, Mingze Bai, Silvano Squizzato, Young Mi Park, Kenneth Haug, Dylan Spalding, Justin Paschall, Noemi del-Toro, Tobias Ternent, Nicola Buso, Reza M Salek, Ugis Sarkans, Robert Petryszak, Maria Keays, Christoph Steinbeck, Rodrigo Lopez, Juan A Vizcaíno & Henning Hermjakob

  2. Institute of Bioinformatics, Chongqing University of Posts and Telecommunications, Chongqing, China

    Mingze Bai

  3. Beijing Proteome Research Center, National Center for Protein Sciences Beijing, Beijing, China

    Mingze Bai & Henning Hermjakob

  4. Department of Pathology, University of Michigan, Ann Arbor, Michigan, USA

    Felipe da Veiga Leprevost, Peng Zhang & Alexey I Nesvizhskii

  5. Research School of Biology, Australian National University, Canberra, Australian Capital Territory, Australia

    Adam J Carroll

  6. Department of Computer Science and Engineering, University of California, San Diego, La Jolla, California, USA

    Mingxun Wang & Nuno Bandeira

  7. Commonwealth Scientific and Industrial Research Organization, Canberra, Australian Capital Territory, Australia

    Peng Zhang

  8. Institute for Systems Biology, Seattle, Washington, USA

    Eric W Deutsch & David S Campbell

  9. Biochemistry & Medical Genetics, University of Manitoba, Winnipeg, Manitoba, Canada

    Ronald C Beavis

  10. Department of Bioengineering, University of California, San Diego, La Jolla, California, USA

    Eoin Fahy, Manish Sud & Shankar Subramaniam

  11. Department of Medicine, University of Cambridge, Cambridge, United Kingdom

    Ariana Barbera

  12. ELIXIR Hub, Wellcome Genome Campus, Hinxton, United Kingdom

    Rafael C Jiménez

  13. Oxford e-Research Centre, University of Oxford, Oxford, United Kingdom

    Susanna-Assunta Sansone

  14. Department of Physiology and Department of Medicine, Division of Cardiology, David Geffen School of Medicine at UCLA, University of California, Los Angeles, Los Angeles, California, USA

    Peipei Ping

  15. Department of Medicine, Division of Cardiology, David Geffen School of Medicine at UCLA, University of California, Los Angeles, Los Angeles, California, USA

    Peipei Ping

Authors
  1. Yasset Perez-Riverol
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  2. Mingze Bai
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  3. Felipe da Veiga Leprevost
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  4. Silvano Squizzato
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  7. Adam J Carroll
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  13. Peng Zhang
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  14. Nicola Buso
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  15. Nuno Bandeira
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  16. Eric W Deutsch
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  17. David S Campbell
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  18. Ronald C Beavis
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  19. Reza M Salek
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  20. Ugis Sarkans
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  21. Robert Petryszak
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  22. Maria Keays
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  23. Eoin Fahy
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  24. Manish Sud
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  25. Shankar Subramaniam
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  26. Ariana Barbera
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  27. Rafael C Jiménez
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  28. Alexey I Nesvizhskii
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  29. Susanna-Assunta Sansone
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  30. Christoph Steinbeck
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  31. Rodrigo Lopez
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  32. Juan A Vizcaíno
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  33. Peipei Ping
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  34. Henning Hermjakob
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Corresponding authors

Correspondence to Yasset Perez-Riverol or Henning Hermjakob.

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The authors declare no competing financial interests.

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Supplementary Figures 1–6, Supplementary Tables 1 and 2 and Supplementary Notes 1–10 (PDF 2411 kb)

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Perez-Riverol, Y., Bai, M., da Veiga Leprevost, F. et al. Discovering and linking public omics data sets using the Omics Discovery Index. Nat Biotechnol 35, 406–409 (2017). https://doi.org/10.1038/nbt.3790

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