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Showing posts from October, 2023

Data Deposition made easy

Bioactivity data in ChEMBL originates from two main sources: biomedical literature and  data entering ChEMBL via data deposition. Over the years, we have seen an increase in deposited data sets (as shown in the Figure above). To make data deposition easier, we recently did some major updates to our deposition guide and supplemented it with a deposition video , and a brief checklist for depositors. Compound structural data must be supplied to the ChEMBL team in CTAB format / as MOL file. If a whole set of structures is supplied, then an SDF file is required. There are several ways to convert a list of SMILES to SDF. One way is to use our public ChEMBL Beaker API. Its functionalities are explained in more detail here and they can be tested interactively here . Just a few lines of code are needed to convert a list of SMILES strings into SD format. from chembl_webresource_client.utils import utils smiles = [ "CCO" , "CC(=O)C1=CC=CC=C1C(=O)O" , "CCN(CC)C(