Except explicitly stated, data available from this interface is under the Creative Commons Attribution 4.0 International license.
The current release of RetroRules is based on MNXref v3.0 for the chemical structures, the reaction definitions and their respective crosslinks to other databases.
Please consider that MNXref information is gathered from different metabolic databases (MetaCyc, KeGG, Bigg, Rhea, ...) and each have different license policies (especially concerning the reuse for commercial purpose). As a consequence, the license related to each individual reaction rule depends of the licensing agreements of the refence database(s) choosen in MNXref to describe each reaction as well as the chemicals involved in it. This information is available at https://www.metanetx.org/mnxdoc/mnxref.html.
Sequence annotations is obtained by cross-referencing MNXref v3.0 with Rhea release 81 and UniProt release 2017_04.
Data explorable through the RetroRules web interface are freely available as a SQLite file: download link (file size is ~2 GB). Details on the SQL schema are provided in the documentation section.
SQLite version for this one is planned but not ready to for publication. However, you can already download the pre-parsed reaction rule files available below ("Download pre-parsed reaction rule files" section)
Pre-parsed reaction rule files can be used as an alternative to the full RetroRules SQLite database. They are ready-to-use files that provide all the non-stereo reaction rules for diameter 2 to 16.
Below are listed the available releases, their specificity and the tools they can be used with. Structure of files are explained into a README file that is provided within each archive.
| Release | Diameters | Hs handling | Tools compatibility | Download |
|---|---|---|---|---|
| rr01 | 2 to 16 | explicit | RetroPath 2.0 |
| Release | Diameters | Hs handling | Tools compatibility | Download |
|---|---|---|---|---|
| rr02 | 2 to 16 | implicit | RetroPath RL | |
| rr02 | 2 to 16 | explicit | RetroPath RL | |
| rr02 | 2 to 16 | explicit | RetroPath 2.0 |
Notice: if you developed an application that make use of one these datasets, please tell us, so and we will add it to the list of compatible tools.