Hi Professor Steinbeck and Dr. Sorokina, Great to hear from you! I've seen the blog posts by Suvee, Swain, and ChemBL. If there are any that I haven't gotten to, I'd love to get a look at them.
By all means, let's set up a call—I'd be glad to learn more about COCONUT and I think describing possible use cases might be easier over the phone. My schedule is completely flexible on Tuesdays, Wednesdays, and Fridays and I'm on US Eastern time. If your schedules permit, let's look into a time next week? Thanks, and looking forward to speaking more. Chris On Thu, Jul 9, 2020 at 3:27 AM Christoph Steinbeck < christoph.steinb...@uni-jena.de> wrote: > 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 > > -- *Christopher Zou * Computer Science and Biochemistry, UC Berkeley '22
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