Hi Chris, we use MongoDB in our COCONUT database of open natural products (https://coconut.naturalproducts.net). For obvious reasons, we use the CDK under the hood, but we are not religious about this and use Rdkit in a lot of our research. We store the chemical structures of natural products and their meta-data (what species they were isolated from, for example). And of course, we have the usual needs for chemical searches, such as identity, substructure and similarity search. The similarity search using as much native MongoDB functionality as possible is an interesting problem. I assume you have seen the few blog posts on this topic. If not, let me know. I am cc-ing Maria Sorokina who works on COCONUT in my team. We would be happy to have a call.
Kind regards, Chris — Prof. Dr. Christoph Steinbeck Analytical Chemistry - Cheminformatics and Chemometrics Friedrich-Schiller-University Jena, Germany Phone Secretariat: +49-3641-948171 http://cheminf.uni-jena.de http://orcid.org/0000-0001-6966-0814 What is man but that lofty spirit - that sense of enterprise. ... Kirk, "I, Mudd," stardate 4513.3.. > On 8. Jul 2020, at 22:59, Christopher Zou <cw...@berkeley.edu> wrote: > > Dear RDKit Community, > > Hope you're all well! I'm a student from UC Berkeley building an integration > between RDKit and MongoDB as part of Google Summer of Code. > > The idea of the project is twofold: > • Provide tools for building a chemically-intelligent MongoDB database. > • Provide high-performance similarity and substructure search that > leverage MongoDB. > If you use or would like to use MongoDB as part of your work, I'd love to get > some input from you, either via email or through a short call. What kinds of > Mongo setups are all of you using? What kinds of information would you like > to store? What are some examples of searches? This would help me build > something as usable as possible for all of you. > > Many thanks—I'm incredibly excited to be contributing to this community. > > Best, > Chris > > > > -- > Christopher Zou > Computer Science and Biochemistry, > UC Berkeley '22 > > _______________________________________________ > Rdkit-discuss mailing list > Rdkit-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss _______________________________________________ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
