IEDB Database Exports (XML/SQL/CSV)

XML Export

The contents of the IEDB are exported weekly to files in XML (Extensible Markup Language) format. The database export page contains a complete database export in XML format along with exports of the various records that are referenced in the complete database export. The complete dataset export is provided as a ZIP archive (iedb_export.zip) containing one XML file for each reference contained in the database. The version 2.x export also contains ZIP archives of XML files that provide users with the full record for the various identifiers that are referenced in the full database export, such as the IEDB accession identifier list, the MHC allele name list, and the organism list. The supporting XML files only contain full records when the record is not otherwise available from the original source.

The database export page also provides the relevant XML Schema Definition (XSD) files for each of the XML files provided. The XSD file(s) for a particular XML file will be located in the second column of the export table. In the case of the complete database export, multiple schemas are provided, with the primary schema being listed first, followed by any supporting schemas.

In addition, an archive of the data as they appeared in IEDB 1.x is available. The archive file, IEDB_2008_4_1_3_28.zip, contains an XML for each reference. The corresponding XSD files are also available for download.

SQL Export

In addition to the XML export, the contents of the IEDB are exported weekly as a MySQL Structure Query Language (SQL) database.  The database export page contains the complete database export in two formats, a single SQL script (iedb_public.sql.gz), and a TAR archive of MyISAM binary tables (iedb_public.tar.gz).  Both export formats are generated from a MySQL v5.0 database server.  The database export page also provides an entity-relationship diagram (ERD) for the MySQL database.

CSV Export

Comma separated values (CSV) file exports are available on-demand from all list pages and list tabs throughout the site.  The CSV file exports are available in two formats, a compact format that only contains the data presented in the list the user is viewing, and a full record format that contains all of the data associated with the records in the list the user is viewing.  For example, reference_compact.zip and reference_full.zip contain the list of all references (literature and submissions) in the database.  The compact version contains reference ID, reference type, PubMed ID, Author(s), Title, Abstract, Journal, and Year.  The full version contains the same information plus author affiliations, Journal volume, Article pages, MeSH terms, and all other reference related information captured in the database.  Files are available for all peptidic epitopes, non-peptidic epitopes, T cell assays, B cell assays, MHC binding assays, MHC ligand elutaion assays, and source organisms.