Retrieving biological knowledge for molecular property prediction

Question

[Lorenzo Fabbri]

I'm working on a project where I try to predict physiological properties of compounds (more precisely drugs). I'd like to enrich the features I'm currently using with more biological knowledge, sort to speak. For instance, one thing that comes to mind is genes and/or pathways associated with each compound.

My question is then the following: are you aware of any web server (that I can access programmatically, this is fundamental) from which given the name of a compound, it retrieves these kind of information? I know it's a very broad question but I still do not know what kind of information could help boost the performance of my current models. The only thing I really need is the possibility to access it programmatically, like from Python.

[Emily]

Please do not cross-post to BioStars and Reddit

Answer 1

[Brice Sarver]

Because of their utility, these databases are usually proprietary and programmatic access, if available, requires a paid subscription.

Here's three off the top of my head:

• COSMIC: free for academics; paid for industry. Has information on drug resistance mutations for somatic cancers.
• Qiagen Knowledge Base: aggregates a bunch of information from a variety of Qiagen's products, including gene-drug relationships.
• Clarivate Analytics: you may be familiar with their Web of Science product, but they also have a discovery-based product called Cortellis.