Data publication and archiving

  • Article
    | Open Access

    Placental dysfunction can have catastrophic or barely discernible effects ranging from miscarriage to apparently normal birth. Here the authors present a comprehensive analysis of the human placental transcriptome and identify circular RNAs and piRNAs.

    • Sungsam Gong
    • , Francesca Gaccioli
    •  & D. Stephen Charnock-Jones
  • Article
    | Open Access

    Modern biological research is complicated by the difficulty of collecting, transforming, annotating, and integrating datasets. Here, the authors present Go Get Data, a fast, reproducible approach to installing standardized data recipes, with an application to genomics data.

    • Michael J. Cormier
    • , Jonathan R. Belyeu
    •  & Aaron R. Quinlan
  • Perspective
    | Open Access

    The IMEx consortium provides one of the largest resources of curated, experimentally verified molecular interaction data. Here, the authors review how IMEx evolved into a fundamental resource for life scientists and describe how IMEx data can support biomedical research.

    • Pablo Porras
    • , Elisabet Barrera
    •  & Sandra Orchard
  • Article
    | Open Access

    Increasing amount of public omics data are important and valuable resources for the research community. Here, the authors develop a set of metrics to quantify the attention and impact of biomedical datasets and integrate them into the framework of Omics Discovery Index (OmicsDI).

    • Yasset Perez-Riverol
    • , Andrey Zorin
    •  & Henning Hermjakob
  • Article
    | Open Access

    Most databases of genotype-phenotype associations are manually curated. Here, Kuleshov et al. describe a machine curation system that extracts such relationships from the GWAS literature and synthesizes them into a structured knowledge base called GWASkb that can complement manually curated databases.

    • Volodymyr Kuleshov
    • , Jialin Ding
    •  & Michael Snyder
  • Review Article
    | Open Access

    Glycomics is gaining momentum in basic, translational and clinical research. Here, the authors review current reporting standards and analysis tools for mass-spectrometry-based glycomics, and propose an e-infrastructure for standardized reporting and online deposition of glycomics data.

    • Miguel A. Rojas-Macias
    • , Julien Mariethoz
    •  & Niclas G. Karlsson
  • Article
    | Open Access

    The validation and analysis of X-ray crystallographic data is essential for reproducibility and the development of crystallographic methods. Here, the authors describe a repository for crystallographic datasets and demonstrate some of the ways it could serve the crystallographic community.

    • Peter A. Meyer
    • , Stephanie Socias
    •  & Piotr Sliz