Download formats

FTP UPDATE:
Most modern browsers (Chrome, Firefox, Safari, etc) have stopped supporting the FTP protocol in the URL's (URL's starting with ftp://). The URL's in this document have been replaced to use HTTPS instead, a protocol that is compatible with modern browsers. However, if you use FTP clients like FileZilla, WinSCP, etc. you are still able to use the FTP URL's to connect.

ChEBI is available from the EBI FTP site. ChEBI can be downloaded in the following formats.

• SDF file
  ChEBI provides its chemical structures and additional data in SDF format. The data is provided in two flavours,
  • Chebi_lite_3star.sdf file contains only the chemical structure, ChEBI identifier and ChEBI Name.
  • ChEBI_complete_3star.sdf file contains all the chemical structures and associated information. Note that it excludes any ontological information as ontological classes are not able to be represented as they do not contain a structure.
  More information about the SDF format used in ChEBI can be found in the Developer Manual.
• Ontology files come in two formats and three versions:
  • OWL - ChEBI provides the ChEBI ontology in the W3C standard Web Ontology Language (OWL) format. Tools such as Protégé, TopBraid, the NeOn toolkit and the OWL-API can be used with this ontology.
  • OBO - ChEBI also provides the ChEBI ontology in OBO format version 1.2. More information about the OBO format can be found on the OBO website or the Gene Ontology website. The tools OBO-edit or Protégé can be used to view the OBO file.
  The versions are:
  • LITE - Only ids, name, subsets and relationships are available. Small size if you are interested in our ontology only
  • CORE - As above plus chemical data (mass, charge, formula) and structures (inchis, inchikeys, smiles)
  • FULL - As above plus name synonyms and manually added cross-reference.
  Nightly update files are now also available.
• Flat file and tab delimited
  ChEBI is stored in a relational database and we currently provide all-star and 3-star ChEBI table in a flat-file tab delimited format. There are various spreadsheet tools available to import this into a relational database. The files are stored in the same structure as the relational database.
• Oracle binary table dumps
  ChEBI provides an Oracle binary table dump that can be imported into an Oracle relational database. You can import this into Oracle using the 'imp' command. The parameter file import.par and import_all_star.par should reside should reside in the same directory when the import is done. The correct command to execute is:
  imp database_name/database_password@Instance_name PARFILE=import_all_star.par
• Generic SQL (Structured Query Language) table dumps
  ChEBI provides a generic SQL dump which consists of SQL insert statements. The archive files called generic_dump_3star.zip and generic_dump_allstar.zip consists of 12 files each which contain SQL table insert statements of the entire database. The file called compounds.sql should always be inserted first in order to avoid any constraint errors. Included in the folder are a MySQL and PostgreSQL create table scripts as an example for other users of the database. These insert statements should be usable in any database which accepts SQL as its query language but has only been tested on MySQL.

Please read the README.txt and the ChEBI Developer Manual where more information is available on the various formats.

Manuals

If you are unable to access the online Google document, please use the FTP link to view our manuals.