Toward a data infrastructure for the Plant Cell Atlas

Abstract

We review how a data infrastructure for the Plant Cell Atlas might be built using existing infrastructure and platforms. The Human Cell Atlas has developed an extensive infrastructure for human and mouse single cell data, while the European Bioinformatics Institute has developed a Single Cell Expression Atlas, that currently houses several plant data sets. We discuss issues related to appropriate ontologies for describing a plant single cell experiment. We imagine how such an infrastructure will enable biologists and data scientists to glean new insights into plant biology in the coming decades, as long as such data are made accessible to the community in an open manner.

Figure 1

The Plant Cell Atlas would sit at the nexus of an interconnected web of databases, in addition to housing data generated by single-cell approaches.

Figure 2

The current Human Cell Atlas Data Coordination Platform (HCA DCP) has evolved from the infrastructure proposed in the HCA white paper (Regev et al., 2018). The three boxes represent different aspects of the DCP (see text). The Plant Cell Atlas logo (depicted at the center of Figure 1) denotes parts of the infrastructure that would require plant-specific ontologies/metadata standards. API, application programming interface; DRS, data repository service; UCSC, University of California Santa Cruz; AWS, Amazon Web Services; EMBL-EBI, European Molecular Biology Laboratory—European Bioinformatics Institute.

Figure 3

Traversing Plant Cell Atlas and other data in an integrated manner, across species. A hypothetical browser would access different data sources, including PCA data, to provide a unified browsing experience for plant biologists who might wish to explore, for example, how equivalent cells in different species respond to the same environmental stimulus.