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. 2017 May 9;35(5):406-409.
doi: 10.1038/nbt.3790.

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

Yasset Perez-Riverol  1 , Mingze Bai  1   2   3 , Felipe da Veiga Leprevost  4 , Silvano Squizzato  1 , Young Mi Park  1 , Kenneth Haug  1 , Adam J Carroll  5 , Dylan Spalding  1 , Justin Paschall  1 , Mingxun Wang  6 , Noemi Del-Toro  1 , Tobias Ternent  1 , Peng Zhang  4   7 , Nicola Buso  1 , Nuno Bandeira  6 , Eric W Deutsch  8 , David S Campbell  8 , Ronald C Beavis  9 , Reza M Salek  1 , Ugis Sarkans  1 , Robert Petryszak  1 , Maria Keays  1 , Eoin Fahy  10 , Manish Sud  10 , Shankar Subramaniam  10 , Ariana Barbera  11 , Rafael C Jiménez  12 , Alexey I Nesvizhskii  4 , Susanna-Assunta Sansone  13 , Christoph Steinbeck  1 , Rodrigo Lopez  1 , Juan A Vizcaíno  1 , Peipei Ping  14   15 , Henning Hermjakob  1   3
Affiliations

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

Yasset Perez-Riverol et al. Nat Biotechnol. .
No abstract available

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Figures

Figure 1
Figure 1
Omics Discovery Index: data standardization, annotation, index and presentation. (a) The datasets stored in public repositories are converted to a common data representation including all metadata and biological entities. The OmicsDI XML files are validated using the OmicsDI XML validator. (b) The OmicsDI XML files are then annotated using public services and databases like UniProt, ChEBI, and PubMed, and the metadata is enriched using the Annotator service. The EBI search engine generates the indexes including other related resources such as PubMed, UniProt, Ensembl and ChEBI. (c) Different clients can use the OmicsDI API to retrieve data from the resource including the web interface and the ddiR package.
Figure 2
Figure 2
Distributions of OmicsDI datasets. (a) Distribution of datasets per omics type and organism category including model organisms, non-model organisms (excluding human) and human. (b) The dataset view showing the other related omics datasets, including the ontology highlighting option to extract the most relevant terms in the metadata. (c) Pearson-correlation plot between the metadata similarity score and the biological similarity score, across transcriptomics (T), proteomics (P) and metabolomics (M) datasets. (d) The shared molecules box shows all datasets with a biological similarity score of more than 0.5, with a slider allowing a user to increase the cutoff value (here set to 0.81).
See this image and copyright information in PMC

References

    1. Bourne PE, Lorsch JR, Green ED. Perspective: Sustaining the big-data ecosystem. Nature. 2015;527:S16–17. - PubMed
    1. Perez-Riverol Y, Alpi E, Wang R, Hermjakob H, Vizcaino JA. Making proteomics data accessible and reusable: current state of proteomics databases and repositories. Proteomics. 2015;15:930–949. - PMC - PubMed
    1. Wilkinson MD, et al. The FAIR Guiding Principles for scientific data management and stewardship. Sci Data. 2016;3:160018. - PMC - PubMed
    1. Prins P, et al. Toward effective software solutions for big biology. Nature biotechnology. 2015;33:686–687. - PubMed
    1. Bourne PE, et al. The NIH Big Data to Knowledge (BD2K) initiative. J Am Med Inform Assoc. 2015;22:1114. - PMC - PubMed

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