Skip to main content

Accessing SureChEMBL data in bulk




It is the peak of the summer (at least in this hemisphere) and many of our readers/users will be on holiday, perhaps on an island enjoying the sea. Luckily, for the rest of us there is still the 'sea' of SureChEMBL data that awaits to be enjoyed and explored for hidden 'treasures' (let me know if I pushed this analogy too far). See here and here for a reminder of SureChEMBL is and what it does. 

This wealth of (big) data can be accessed via the SureChEMBL interface, where users can submit quite sophisticated and granular queries by combining: i) Lucene fields against full-text and bibliographic metadata and ii) advanced structure query features against the annotated compound corpus. Examples of such queries will be the topic of a future post. Once the search results are back, users can browse through and export the chemistry from the patent(s) of interest. In addition to this functionality, we've been receiving user requests for local (behind the firewall), batch access of the SureChEMBL data almost since day one of releasing the interface last year. By such data, we mean not only the compound repository (which is available anyway) but also the comprehensive map of associations between compound and patents, i.e. which compound was extracted from which section of which patent, for all available compounds and patents. To address these requests, we currently provide two additional ways to access the SureChEMBL data:

1) The map file. This is a flat file including compound, patent and association information. The back file contains all associations for eligible patent documents published between 1960 and 2014. Since then, two more incremental update files have been available covering the first 2 quarters of 2015. More info on the structure of the file is found here and all files are available here. We will continue to add incremental updates quarterly. 

2) The data client. This is a script that firstly creates a relational database in the user's environment and then populates the database with SureChEMBL data it retrieves from our private ftp server on a nightly basis. In addition to the front file (the patent and compound info that arrives daily), the script can also fetch the back file for each past year and back-fill the database accordingly. In the end, the data client script effectively creates a local and live snapshot of the SureChEMBL database, which allows for further integration, querying, filtering, deployment, etc., on the users' side. More info on the details of the client can be found here and documentation on how to set the client up is available here. Note that the script will need credentials to access our private ftp server, which we are happy to provide if you ask. It is also worth mentioning that the data client provides more information in a more timely fashion than the map file (daily vs. quarterly) but it requires considerably more effort and resources to set it up, compared to reading a flat file. 

As usual, this is not all - there is soon going to be an additional way to batch-access the SureChEMBL data. As announced recently, an enhanced version of SureChEMBL data (chemical AND biological annotations from patents), will be semantically integrated in the OpenPHACTS system and will be part of the freely available OpenPHACTS API. This will be available later this year.


George

Comments

Popular posts from this blog

ChEMBL & SureChEMBL anniversary symposium

  In 2024 we celebrate the 15th anniversary of the first public release of the ChEMBL database as well as the 10th anniversary of SureChEMBL. To recognise this important landmark we are organising a two-day symposium to celebrate the work achieved by ChEMBL and SureChEMBL, and look forward to its future.   Save the date for the ChEMBL 15 Year Symposium October 1-2, 2024     Day one will consist of four workshops, a basic ChEMBL drug design workshop; an advanced ChEMBL workshop (EUbOPEN community workshop); a ChEMBL data deposition workshop; and a SureChEMBL workshop. Day two will consist of a series of talks from invited speakers, a few poster flash talks, a local nature walk, as well as celebratory cake. During the breaks, the poster session will be a great opportunity to catch up with other users and collaborators of the ChEMBL resources and chat to colleagues, co-workers and others to find out more about how the database is being used. Lunch and refreshments will be pro

ChEMBL 34 is out!

We are delighted to announce the release of ChEMBL 34, which includes a full update to drug and clinical candidate drug data. This version of the database, prepared on 28/03/2024 contains:         2,431,025 compounds (of which 2,409,270 have mol files)         3,106,257 compound records (non-unique compounds)         20,772,701 activities         1,644,390 assays         15,598 targets         89,892 documents Data can be downloaded from the ChEMBL FTP site:  https://ftp.ebi.ac.uk/pub/databases/chembl/ChEMBLdb/releases/chembl_34/ Please see ChEMBL_34 release notes for full details of all changes in this release:  https://ftp.ebi.ac.uk/pub/databases/chembl/ChEMBLdb/releases/chembl_34/chembl_34_release_notes.txt New Data Sources European Medicines Agency (src_id = 66): European Medicines Agency's data correspond to EMA drugs prior to 20 January 2023 (excluding vaccines). 71 out of the 882 newly added EMA drugs are only authorised by EMA, rather than from other regulatory bodies e.g.

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