Focus on Drug/Compound Networks

Posted by Rudi Pillich


In an effort to provide usable data in the form of biological networks, the NDEx Project has developed a content plan that aims to provide access to a vast array of drug/compound data from several different databases.

To date, the NDEx Public Server offers a selection of networks from DrugBank, Therapeutic Target Database (TTD) and Binding DB. All networks were generated from the latest data sets available and will be updated quarterly.

It is important to point out that networks in NDEx are not just full database dumps, but rather a selection of the database content that we think can be useful and usable by researchers in different fields.

For example, we have queried the Binding DB and generated data subsets that are more manageable and of higher significance: it is in fact of limited interest to have a network with compounds that have very low affinity for their targets, while it is a lot more meaningful to operate on a network that only contains commercially available compounds that bind "mouse" targets with high (<10 nM) affinity.

Our content plan also includes data form the Comparative Toxicogenomics Database (CTD), VenomKB, and Go to Pharmacology database (GtoP db): networks from these sources will be available in the next couple of weeks.

NDEx users can easily find drug/compound-related networks searching our Public Server in several ways:

  • Using the database name (i.e. DrugBank or BindingDB).
  • Using generic search terms like "compounds" or "drugs"
  • Using disease, target and drug/compound names or identifiers (i.e. PubChem CID, UniProt ID, NCBI gene symbol, etc.)

Look for the NDEx collection of drug/compound networks to keep growing and include new data sources. And remember that we want to hear from you…

Do you think a specific drug/compound database should be added to our list? Would you like NDEx to include data sets from your favorite database? Or perhaps help you generate a network out of your own data?

Get in touch with us, let us hear your voice and we will do our best to accommodate your requests!