For commongroups to work, it needs a database of compounds searchable by chemical structure. Specifically, this must be a PostgreSQL database with the RDKit extension. We do not distribute a pre-built database, and there are no requirements for or limits on what compounds and data sources might be included in the database.

We develop and test commongroups using a database compiled from public data available in the US EPA CompTox Dashboard, containing approximately 700,000 structures. We believe that this is a good starting point for our immediate goals. We distribute a program that can automatically download data and recreate the particular database that we use.

What follows is a general description of how a database can be created and prepared for use with commongroups.

Data sources

From the US EPA CompTox Dashboard:

  • dsstox_20160701.tsv - Downloaded as
    • Date: 2016-07-01 (file generated); 2016-12-14 (posted on EPA website)
    • Accessed: 2017-04-18
    • Contains mappings between the DSSTox substance identifier (DTXSID) and the associated InChI/InChIKey.
  • Dsstox_CAS_number_name.xlsx
    • Date: 2016-11-14
    • Accessed: 2017-04-18
    • Contains the CASRN, DTXSID, and the “preferred name” used by US EPA.
  • PubChem_DTXSID_mapping_file.txt
    • Date: 2016-11-14
    • Accessed: 2017-04-18
    • Contains the PubChem SID, PubChem CID and DTXSID.

Constructing the database

These are the general steps to create the database using the data sources above:

  1. Create a database table of DTXSIDs, InChI(Key)s, and RDKit mol-type representations of the structures (based on InChI)
  2. Create database tables with DTXSID-CASRN and DTXSID-CID correspondences.
  3. Merge the above tables on DTXSID, creating either a new table or a materialized view. Create an index on molecular structures using the GiST-powered RDKit extension.

To execute these steps automatically on your system, first install the required software and then see Automated database instantiation. For more technical detail and the exact database commands used, please see the source code in tools/

Known limitations

Currently, for commongroups to be able to use a database, it must contain a table or view called compounds, which in turn must contain a column called molecule, containing molecular structures in the RDKit mol data type. Furthermore, for HTML display of compound groups, the program currently assumes that compounds contains the following columns: cid (PubChem CID, also used for images), casrn, and dtxsid. This may change in future versions.

The database produced by our automatic installation script satisfies these requirements.