ChEBI is available from the EBI FTP site.
ChEBI can be downloaded in the following formats.
Please read the README.txt and the ChEBI Developer Manual where more information is available on the various formats.
- SDF file
ChEBI provides its chemical structures and additional data in SDF format.
The data is provided in two flavours,
More information about the SDF format used in ChEBI can be found in the Developer Manual.
- 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.
- OWL file
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 file
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 tool OBO-edit can be used to view the OBO file.
- 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
- 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.