ImmPort, toward repurposing of open access immunological assay data for translational and clinical research

Abstract

Immunology researchers are beginning to explore the possibilities of reproducibility, reuse and secondary analyses of immunology data. Open-access datasets are being applied in the validation of the methods used in the original studies, leveraging studies for meta-analysis, or generating new hypotheses. To promote these goals, the ImmPort data repository was created for the broader research community to explore the wide spectrum of clinical and basic research data and associated findings. The ImmPort ecosystem consists of four components-Private Data, Shared Data, Data Analysis, and Resources-for data archiving, dissemination, analyses, and reuse. To date, more than 300 studies have been made freely available through the Shared Data portal (www.immport.org/immport-open), which allows research data to be repurposed to accelerate the translation of new insights into discoveries.

Figure 1. ImmPort Data Flow.

The ImmPort ecosystem is composed of four applications: Private Data, Shared Data, and Data Analysis and Resources. Private Data is the data acquisition and curation site, Shared Data supports searching and distribution of data, Data Analysis provides a graphic interface for open source data management and analysis tools primarily focused on flow cytometry results, and Resources provides advanced data analysis tools, tutorials, documentation. This schematic representation shows the steps of data capture, data curation, and secondary usage of ImmPort studies by different entities. The solid line denotes an example flow of cytometry data across the four applications.

Figure 2. ImmPort Data Model.

This figure illustrates the relationship between the nodes linking to a detailed description of the term in the ImmPort data model. The color of nodes represents the types of information stored in the ImmPort database tables.

Figure 3. ImmPort Tutorials.

The ImmPort team maintains a library of tutorials under the Resources application to highlight the programing tools used to explore, retrieve and analyze shared data (http://immport.org/resources/tutorials).

Figure 4. ImmPortGalaxy.

The ImmPort Data Analysis application offers a platform to run command line analysis tools with a graphical user interface. ImmPort Galaxy supports creation and editing of workflows, tools chained together in a user-defined fashion (a) Available tools allow users to go from Flow Cytometry Data basic exploration (b) to multi-sample analysis (c, d).