Metrabase

Metabolism and Transport Database

Download

  • Metrabase
    Version 1.0 of the database (i.e. its MySQL dump) is available for download here. To load the database from a dump file, you should first create a database on your system and then load the dump file, for example like this:
    # tar -xzvf metrabase1_0.tar.gz
    # mysql -u username -p
    mysql> CREATE DATABASE metrabase;
    # mysql -u username -p metrabase < metrabase1_0.sql

  • User manual
    The Metrabase manual is available here.

  • Transporter substrate dataset
    Each version of the transporter substrate dataset (MBTPsubDS) contains interactions between small molecules and transporters, and includes all the unique substrate and non-substrate records obtained from Metrabase and processed to facilitate human transporter data analysis and predictive modelling. By 'unique' we mean the unique (cmpd_id, protein_id, action_type) tuples. Mixtures, coordination complexes, all inorganic compounds, polymers and metalloid-containing compounds (including Se-containing compounds) were excluded. Stereoisomers were not considered and all multi-component structures were replaced by their single-component counterparts (effectively, this corresponds to the usually applied procedure of keeping just the largest component of each structure, except that this procedure if based on either the number of atoms or molecular mass can lead to retention of unwanted components). Structures with a molecular mass of > 1 kDa were also removed, thus leaving only small organic molecules in the dataset (their structures are provided as SMILES strings). Finally, all the duplicates formed due to ignored stereoisomerism and salt components were removed.

    MBTPsubDS1 (based on Metrabase version 1.0) - all the interactions involving conflicting action types (where a compound was found to be both a substrate and a non-substrate of a single transporter) were excluded.
    MBTPsubDS1a (based on Metrabase version 1.0) - some of the conflicting action types were resolved upon our evaluation of such records and the corresponding compound-protein pairs were added to MBTPsubDS1 where we thought we could consider the compound as either a substrate or a non-substrate.