With the release of IEDB v2.0, the primary identifier used for epitopes was changed. In the previous v1.x versions of IEDB, the IEDB ID was the primary identifier for epitopes. The IEDB ID was a unique identifier given to every epitope in context of its reference, i.e., the same sequence was given a different IEDB ID for each reference it was found in. In an effort to reduce data redundancy and improve identifier stability, the v2.0 release of the IEDB collapses epitope records and only reports distinct epitopes with a new identifier, the Epitope ID. The following files have been produced to aid developers in transitioning from the old IEDB ID to the new Epitope ID:
IedbId2EpitopeId.csv: This file provides a mapping from the previous IEDB ID to the current Epitope ID for all records where a direct mapping1 is available. The file is in a standard CSV format with two fields, the IEDB ID and its corresponding Epitope ID.
IedbIdWithoutDirectMapping.csv: Although the majority of IEDB IDs map directly to Epitope IDs, some do not2. This file provides a list of all IEDB IDs that do not have a direct mapping to an Epitope ID, alternative mappings may or may not exist and additional information is provided in the files below.
IedbIdAltEpitopeId.csv: This file contains a mapping from IEDB IDs to Epitope IDs in cases where the IEDB ID is no longer publicly available but there is a distinct epitope available that contains the same epitope information as the original IEDB ID, but from a different reference. The file is in a standard CSV format with two fields, the IEDB ID and a corresponding Epitope ID.
IedbIdNoMapping.csv: This file provides a list of all IEDB IDs that do not have any mapping to an Epitope ID. We are regularly adding new epitopes and continuing to improve the quality of old records, therefore records contained in this list may be mapped in the future. The files available here will be updated as new mappings become available so it is recommended that developers subscribe to this topic if they have records that need to be updated but no mapping is currently available.
1A direct mapping is one where the record associated with the IEDB ID is in the IEDB system and has been collapsed into a distinct epitope record. This collapsing is tracked so a direct mapping of IEDB ID to Epitope ID can be provided.
2During the migration from v1.x to v2.0 several records were recurated. During this recuration some records were removed and some records were recreated. This recuration resulted in some IEDB IDs no longer being publicly available. This instability of IEDB IDs was part of the motivation for migrating to the new Epitope ID, which provides more stability in the record identifiers.