Copyright©2009 Antony Williams
For those of you who read this blog you will be aware that it can take a lot of time just to get a single chemical curated against its correct associations of chemical names and synonyms. I’ve shown this for vancomycin, Taxol (1,2,3), Ginkgolide B and it is presently underway with Digitonin, though not yet complete. Working on one structure is hard enough. Building a database of a few thousand curated structures is difficult work yet the EBI did it, and did it well when they built ChEBI. ChEBI is also not perfect as we discovered working on vancomycin and I still find occasional small issues.
The EBI recently released the ChEMBL database. This is a much bigger resource as described at the home page for the resource here. The site states “ChEMBL is a database of ca. 500,000 bioactive compounds, their quantitative properties and bioactivities (binding constants, pharmacology and ADMET, etc). The data is abstracted and curated from the primary scientific literature and the data made available due to funding by the Wellcome Trust.” It is MUCH harder to curate larger databases and 1/2 a million records is a challenge.
I downloaded the data from the FTP site and took a browse of the data. There are definitely structures in the data file that we don’t have in ChemSpider but I found an issue with charge balance for many hundreds of records where the counterions were charged (for example, chloride or bromide) but the primary component was neutral. An example is here where the compound is named as a hydrochloride but the compound has the chloride anion. I think this likely arises from treatment with some type of standardizer so it should be a matter of changing the standardizer settings and regenerating. We deal with over 23 million compounds and have been through such issues ourselves when it comes to generation of structure images.
For an example of a rich record in ChEMBL take a look at this record showing the target, assay, activity type, value and reference all listed. ChEMBL is sure to be an invaluable reference for the Life Sciences.Stumble it!