3
$\begingroup$

I am looking for extensions/add-ons for relational databases (RDBMS) that enable storing and handling chemical structures including the possibility for substructure searches and similarity search.

I am currently dealing with a custom application that is built on top of an Oracle 11gR2 database with the OrChem extension. In the words of the accompanying scientific publication, OrChem is

[..] an extension for the Oracle 11G database that adds registration and indexing of chemical structures to support fast substructure and similarity searching.

This is what the application needs.

The problem is that OrChem does not seem to be maintained anymore, the last release happened almost 10 years ago. From what little I could find in my research, I got the impression that OrChem also only seems to play nice with Oracle 11G, which will soon reach the end of its extended support lifecycle.

So, since I have the need to upgrade the underlying database, I am looking for information on alternatives (or, if someone can offer, experiences with running OrChem with versions >= Oracle 12).

For possible alternatives, projects that I could find are

  • MyChem, an extension similar to OrChem for the MySQL database (versions >= 4.0) and MariaDB. Of the projects I could find, this one is the least outdated, but even that means that the last release happened 6 years ago.

  • Pgchem::tigress, a cheminformatics extension for the PostgreSQL DBMS (version > 8.x). Similarly to OrChem, the last commit happened almost 10 years ago.

  • chemsearch, for which again, the last release happened about 10 years ago. This one seems to be relatively mature (version number is 3.2) and it supports at least the Oracle and PostgreSQL RDBMS, the source code zip also has folders named mssql and mysql. However, since I could not find a real documentation, I am unsure which versions of the different RDMBS are actually supported.

Can anyone offer deeper insights concerning the compatibility of the listed cheminformatics extensions with concrete RDBMS versions and/or more current alternatives that are not listed here?

Improve this question
$\endgroup$
1
  • 1
    $\begingroup$ You do not specify the type of molecules. If these are small and deposit as SMILES strings, you may consider to compute fingerprints for a subsequent similarity search. See, e.g., this entry from the OpenBabel documentation, or Greg Landrum's presentation at RDKit user group meeting 2012 here. $\endgroup$
    – Buttonwood
    Commented Oct 28, 2021 at 17:52

1 Answer 1

Reset to default
4
$\begingroup$

It seems that my search was missing the correct keyword. The database extension modules I was looking for are usually called cartridges.

A search for rdbms chem cartridge yielded a few more recent options:

This list is not meant to be exhaustive, just thought I'd share what I could find already with little effort.

Improve this answer
$\endgroup$
1

Not the answer you're looking for? Browse other questions tagged or ask your own question.