Download Questions

I want to download the ChEMBL database and run a query. How can I get started?

You can download the database here. You could try our SQLite version. You might already have a browser for this installed on your system, but if not, you can download one here. It's simple to install, and just use 'Open Database' to load the unzipped chembl file. Then you can execute SQL queries or browse the ChEMBL tables.

Is there a file that I can download from the FTP site that contains ALL of the bioactivity data?

MySQL, PostgreSQL and SQLite dumps provide all data in ChEMBL. Please note that PostgreSQL and MySQL dumps requires the user to install a database instance.

Can I download an SDFile of compounds and associated bioactivity from the interface?

You cannot download a single SDFile of the compound information including the structure, alongside the bioactivity data.

Is there a password on the PostgreSQL or MySQL data upload?

No there is no password set for this, so if you are asked for a password it is likely to be a local database instance issue and you will need to contact your database administrators to gain access.

What GB of space is required to upload the data dump files into PostgreSQL and MySQL ?

You will need around 35GB of free space available to import the ChEMBL dump files.

What's the difference between the SDFile and the MySQL/PostgreSQL/SQLite downloads on your FTP server?

The SDfile contains the structures and the IDs of all the compounds currently found in the database. The MySQL/PostgreSQL/SQLite downloads contain all the compounds and associated bioactivities, but needs to be uploaded into a database to be viewed properly.

I get an error message when trying to download some data from the interface.

If you get an error message, please send an email to [e-mail], or create an issue in our GitHub repository. We recommend that you include the full url of the page in your message, this helps us to identify the problem.

What is the expiration date in the downloads from the interface?

When a user generates a download from the interface, the file is kept in our servers for 7 days after the file was created. For example, if a file was generated on 17th May at 8:00 AM, it will be kept in our servers until 24th May at 8:00 AM. This means that if the same download is requested again during that period, the file will not be generated again and it will be ready to be downloaded immediately. The times shown are always based in the UTC timezone.

During the period in which we keep the downloaded file, we also keep the original query parameters required to generate the file. The parameters and the file itself are deleted after the expiration time has passed. It is important to make clear that we don't save any data that can be used to identify the user generating the file. We save just the necessary data to be able to provide the service.