Skip to main content

ChEMBL Amazon Web Services


We have started to use Amazon Web Services (AWS) for a number of mini projects in the group. As part of this work we have created ChEMBL Amazon Machine Image (AMI), which we have decided to make publicly available. The ChEMBL AMI is based on the 64-bit Amazon Linux AMI, but additional comes installed with a MySQL server, which contains the ChEMBL_09 database. The benefit of making this available is that a user can have a MySQL instance up and running in a matter minutes and at almost no cost if the service is run on the AWS Free Usage Tier.

To create an instance based on the ChEMBL AMI, go through the following steps:
  1. Set up an AWS account (note you will need an existing Amazon account or credit card to do this).
  2. Login to the AWS Management Console
  3. Change Region to EU West (Ireland). Currently the ChEMBL AMI is only available to instances running in this region.
  4. Go to EC2 tab and click on Launch Instance button. The Create Instance Wizard should appear.
  5. On the CHOOSE AN AMI section select the Community AMIs tab and enter "chembl" in the search box. Only 1 public AMI should appear (ami-cf91a6bb), click the select button.
  6. On the INSTANCE DETAILS section, make sure you select Mirco instance type if you want to use the Free Usage Tier
  7. Proceed through CREATE KEY PAIR and CONFIGURE FIREWALL sections of the wizard and you are done


The MySQL instance will be up running and a user named chembluser (password:chembluser, we recommend you change this) has been setup with access to the chembl_09 database. So you should be able to connect to your MySQL database with the following command:

mysql -h xxxxxxxxxxxxxxxxx.compute.amazonaws.com -u chembluser -pchembluser chembl_09

(The command above assumes you have access to your instance on port 3306 from the ip range you are working from. This can be configured in the Security Groups section of the AWS Management Console).

If this proves to be a useful resource to the users of the ChEMBL data we will make publicly available AMIs for future ChEMBL database releases.

Comments

Popular posts from this blog

A python client for accessing ChEMBL web services

Motivation The CheMBL Web Services provide simple reliable programmatic access to the data stored in ChEMBL database. RESTful API approaches are quite easy to master in most languages but still require writing a few lines of code. Additionally, it can be a challenging task to write a nontrivial application using REST without any examples. These factors were the motivation for us to write a small client library for accessing web services from Python. Why Python? We choose this language because Python has become extremely popular (and still growing in use) in scientific applications; there are several Open Source chemical toolkits available in this language, and so the wealth of ChEMBL resources and functionality of those toolkits can be easily combined. Moreover, Python is a very web-friendly language and we wanted to show how easy complex resource acquisition can be expressed in Python. Reinventing the wheel? There are already some libraries providing access to ChEMBL d

ChEMBL 29 Released

  We are pleased to announce the release of ChEMBL 29. This version of the database, prepared on 01/07/2021 contains: 2,703,543 compound records 2,105,464 compounds (of which 2,084,724 have mol files) 18,635,916 activities 1,383,553 assays 14,554 targets 81,544 documents Data can be downloaded from the ChEMBL FTP site:   https://ftp.ebi.ac.uk/pub/databases/chembl/ChEMBLdb/releases/chembl_29 .  Please see ChEMBL_29 release notes for full details of all changes in this release: https://ftp.ebi.ac.uk/pub/databases/chembl/ChEMBLdb/releases/chembl_29/chembl_29_release_notes.txt New Deposited Datasets EUbOPEN Chemogenomic Library (src_id = 55, ChEMBL Document IDs CHEMBL4649982-CHEMBL4649998): The EUbOPEN consortium is an Innovative Medicines Initiative (IMI) funded project to enable and unlock biology in the open. The aims of the project are to assemble an open access chemogenomic library comprising about 5,000 well annotated compounds covering roughly 1,000 different proteins, to synthesiz

Identifying relevant compounds in patents

  As you may know, patents can be inherently noisy documents which can make it challenging to extract drug discovery information from them, such as the key targets or compounds being claimed. There are many reasons for this, ranging from deliberate obfuscation through to the long and detailed nature of the documents. For example, a typical small molecule patent may contain extensive background information relating to the target biology and disease area, chemical synthesis information, biological assay protocols and pharmacological measurements (which may refer to endogenous substances, existing therapies, reaction intermediates, reagents and reference compounds), in addition to description of the claimed compounds themselves.  The SureChEMBL system extracts this chemical information from patent documents through recognition of chemical names, conversion of images and extraction of attached files, and allows patents to be searched for chemical structures of interest. However, the curren

Julia meets RDKit

Julia is a young programming language that is getting some traction in the scientific community. It is a dynamically typed, memory safe and high performance JIT compiled language that was designed to replace languages such as Matlab, R and Python. We've been keeping an an eye on it for a while but we were missing something... yes, RDKit! Fortunately, Greg very recently added the MinimalLib CFFI interface to the RDKit repertoire. This is nothing else than a C API that makes it very easy to call RDKit from almost any programming language. More information about the MinimalLib is available directly from the source . The existence of this MinimalLib CFFI interface meant that we no longer had an excuse to not give it a go! First, we added a BinaryBuilder recipe for building RDKit's MinimalLib into Julia's Yggdrasil repository (thanks Mosè for reviewing!). The recipe builds and automatically uploads the library to Julia's general package registry. The build currently targe

New Drug Warnings Browser

As mentioned in the announcement post of  ChEMBL 29 , a new Drug Warnings Browser has been created. This is an updated version of the entity browsers in ChEMBL ( Compounds , Targets , Activities , etc). It contains new features that will be tried out with the Drug Warnings and will be applied to the other entities gradually. The new features of the Drug Warnings Browser are described below. More visible buttons to link to other entities This functionality is already available in the old entity browsers, but the button to use it is not easily recognised. In the new version, the buttons are more visible. By using those buttons, users can see the related activities, compounds, drugs, mechanisms of action and drug indications to the drug warnings selected. The page will take users to the corresponding entity browser with the items related to the ones selected, or to all the items in the dataset if the user didn’t select any. Additionally, the process of creating the join query is no