FAIR principles and the IEDB: short-term improvements and a long-term vision of OBO-foundry mediated machine-actionable interoperability

Abstract

The Immune Epitope Database (IEDB), at www.iedb.org, has the mission to make published experimental data relating to the recognition of immune epitopes easily available to the scientific public. By presenting curated data in a searchable database, we have liberated it from the tables and figures of journal articles, making it more accessible and usable by immunologists. Recently, the principles of Findability, Accessibility, Interoperability and Reusability have been formulated as goals that data repositories should meet to enhance the usefulness of their data holdings. We here examine how the IEDB complies with these principles and identify broad areas of success, but also areas for improvement. We describe short-term improvements to the IEDB that are being implemented now, as well as a long-term vision of true 'machine-actionable interoperability', which we believe will require community agreement on standardization of knowledge representation that can be built on top of the shared use of ontologies.

Figure 1.

Abbreviated IEDB record for one assay. The data shown are an abbreviated version of the IEDB record for http://www.iedb.org/assay/1288921. The record is separated into sections (e.g. Reference, Epitope, Immunization), and subsections (e.g. Host within the Immunization section). The leftmost column contains a numeric ID for ease of reference in this manuscript that is not part of the IEDB. A representative subset of 38 of the original 63 data rows of the record are displayed, and some rows were re-ordered to improve readability of this table.