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.
Highlights
The principles of Findability, Accessibility, Interoperability and Reusability (FAIR; Textbox 1) have been formulated as critical goals that data repositories should meet to enhance the usefulness of their data holdings (1)
Textbox 1: The FAIR principles as stated in the study by Wilkinson et al (1) To be Findable: F1.data are assigned a globally unique and persistent identifier F2. data are described with rich metadata F3. metadata clearly and explicitly include the identifier of the data it describes F4.data are registered or indexed in a searchable resource To be Accessible: A1.data are retrievable by their identifier using a standardized communications protocol A1.1 the protocol is open, free, and universally implementable A1.2 the protocol allows for an authentication and authorization procedure, where necessary A2. metadata are accessible, even when the data are no longer available To be Interoperable: I1.data use a formal, accessible, shared, and broadly applicable language for knowledge representation
In the case of the information stored in the Immune epitope structure itself (Epitope) Database (IEDB), there is no separation between data and metadata
Summary
The principles of Findability, Accessibility, Interoperability and Reusability (FAIR; Textbox 1) have been formulated as critical goals that data repositories should meet to enhance the usefulness of their data holdings (1). Following the example of other responsible databases such as UniProt (2), we wanted to assess how well the Immune Epitope Database (IEDB) (3) currently adheres to FAIR principles and how it could be further improved. In this context, it is important to note some characteristics of the IEDB in order to understand how it compares to other knowledge resources. Our user community predominantly consists of experimental scientists, so most of the effort to date has gone into making the query
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