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F1000Res. 2019 Jan 7;8:21. doi: 10.12688/f1000research.17518.1. eCollection 2019.

restfulSE: A semantically rich interface for cloud-scale genomics with Bioconductor.

Author information

1
Channing Division of Network Medicine, Harvard Medical School, Boston, Massachusetts, 02115, USA.
2
Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA, 02115, USA.
3
Fred Hutchinson Cancer Research Center, Seattle, Washington, 98109, USA.
4
Tools and Cloud Technology, HDF Group, Seattle, WA, 98109, USA.
5
Center for Cancer Research, National Cancer Institute, USA, Bethesda, Maryland, 20892, USA.
6
Epidemiology and Biostatistics, CUNY School of Public Health, New York, New York, 10027, USA.
7
Biostatistics and Bioinformatics, Roswell Park Cancer Institute, Buffalo, New York, 14203, USA.

Abstract

Bioconductor's SummarizedExperiment class unites numerical assay quantifications with sample- and experiment-level metadata.  SummarizedExperiment is the standard Bioconductor class for assays that produce matrix-like data, used by over 200 packages.  We describe the restfulSE package, a deployment of  this data model that supports remote storage.  We illustrate use of SummarizedExperiment with remote HDF5 and Google BigQuery back ends, with two applications in cancer genomics.  Our intent is to allow the use of familiar and semantically meaningful programmatic idioms to query genomic data, while abstracting the remote interface from end users and developers.

KEYWORDS:

BigQuery; Bioconductor; Bioinformatics; HDF5; REST APIs

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