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. 2020 Apr 15;36(8):2636-2642.
doi: 10.1093/bioinformatics/btz959.

The ELIXIR Core Data Resources: fundamental infrastructure for the life sciences

Rachel Drysdale  1 , Charles E Cook  2 , Robert Petryszak  2 , Vivienne Baillie-Gerritsen  3 , Mary Barlow  2 , Elisabeth Gasteiger  3 , Franziska Gruhl  4 , Jürgen Haas  5 , Jerry Lanfear  1 , Rodrigo Lopez  2 , Nicole Redaschi  3 , Heinz Stockinger  4 , Daniel Teixeira  4   6 , Aravind Venkatesan  2 ; Elixir Core Data Resource Forum; Niklas Blomberg  1 , Christine Durinx  4 , Johanna McEntyre  2
Collaborators, Affiliations

The ELIXIR Core Data Resources: fundamental infrastructure for the life sciences

Rachel Drysdale et al. Bioinformatics. .

Abstract

Supplementary data are available at Bioinformatics online.

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Figures

Figure 1.
Figure 1.
Scale of the Core Data Resources. Cumulative number of data entries in all Core Data Resources, plotted in conjunction with usage (as measured via the number of unique IP addresses accessing the CDRs per month), and the number of staff at the CDRs (as measured by Full Time Equivalents), per year
Figure 2.
Figure 2.
Usage of ELIXIR Core Data Resources in research. Left axis: Sum of the number of mentions of the names of the resources (16 CDRs) and the resource entry identifiers (12 CDRs), per year, in the open access literature. Right axis: citations of pre-identified Key Articles describing the respective resources (18 CDRs). Note that citation data for 2018 are not depicted, as these were not available at the time the analysis for this figure was carried out
Figure 3.
Figure 3.
Cumulative citation counts, to 15th August 2018, for the categories of scientific fields in which the 20 journals that most frequently cite the Core Data Resources are active
Figure 4.
Figure 4.
Core Data Resource interconnectivity. The Core Data Resources are placed on the circumference of the circle, with each resource represented by an arc proportional to the total number of types of data directly exchanged between the two resources. The width of each internal arc, which transects the circle and connects two different resources, is proportional to the number of links between the two resources at the ends of the arc
Figure 5.
Figure 5.
Heat map of the pairwise co-citation of the 12 ELIXIR Core Data Resources that are most frequently co-cited: ArrayExpress, CATH, ENA. Ensembl, HPA, InterPro, PDBe, PRIDE. SILVA, STRING-db, IMEx and UniProt. The intensity of shading correlates with the frequency of co-citation
Figure 6.
Figure 6.
Horizon of assured funding: number of Full Time Equivalent positions at the CDRs from 2014 to 2018 (solid columns) and number of FTEs for which funding is assured 2019 to 2024 (striped columns), by year
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References

    1. Anderson W.P. and Global Life Science Data Resources Working Group. (2017) Data management: a global coalition to sustain core data. Nature, 543, 179–179. - PubMed
    1. Athar A. et al. (2019) ArrayExpress update - from bulk to single-cell expression data. Nucleic Acids Res., 47, D711–D715. - PMC - PubMed
    1. Berman H.M. (2008) The Protein Data Bank: a historical perspective. Acta Crystallogr. A, 64, 88–95. - PubMed
    1. Blomberg N. and ELIXIR Consortium (2017) ELIXIR position paper on FAIR data management in the life sciences [version 1; not peer reviewed]. F1000Research, 6, 1857.
    1. Bourne P.E. et al. (2015) Perspective: sustaining the big-data ecosystem. Nature, 527, S16–17. - PubMed

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