Skip to main content

ChEMBL Web Service Update 3: Image Rendering Changes

By


If you are a follower of this blog you will have seen some earlier posts (here and here) providing details on changes we are making to our Web Services. I recommend reviewing the previous posts, but in summary we have setup a temporary base URL to allow existing ChEMBL Web Service users to test the new ChEMBL API powered Web Services. The new temporary base URL is:

https://www.ebi.ac.uk/chemblws2

As well as providing users with all existing functionality we have also added a couple of extra features, one of which is improved molecule rendering options. The current live Web Services provides the following REST call to allow you to get a molecule image: 

https://www.ebi.ac.uk/chemblws/compounds/CHEMBL192/image

  

You are able to provide a dimension argument (pixels) to change the size of the image:


The image quality has deteriorated, this is because the image returned is simply re-sized version of the first image. The new ChEMBL API powered Web Services addresses this issue by dynamically generating the images, using either the RDKit or the Indgio chemistry toolkits (defaults to RDKit). So, to get an image using the new services, you just need to add '2' to the base URL:

 

When using the dimensions argument with the new Web Services you now get the following improved smaller image:

The coordinates used to generate the image are based on those found in the ChEMBL192 molfile. All current ChEMBL images are produced using Pipeline Pilot, which is currently setup to ignore the molfile coordinates and layout molecule how it sees best. This explains why the layout of the first two images are different to the second two. We can get the new Web Services to ignore coordinates and get the chemical toolkit to layout molecule coordinates how it sees best using the ignoreCoords=1 argument:

If you would prefer to use Indigo to generate your ChEMBL molecule images you can use the engine argument:

Finally, it is also possible to use any combination of the 3 arguments mentioned above:

https://www.ebi.ac.uk/chemblws2/compounds/CHEMBL192/image?engine=indigo&ignoreCoords=1&dimensions=200

 

In summary, the new Web Service base URL extends the the current image generating functionality, by improving the dimensions argument and introducing the ignoreCoords and engine arguments. More details in table below:

Argument Name Argument Description Argument Options Default
dimensions Size of image in pixels 1-500 500
ignoreCoords Choose to use or ignore coordinates in ChEMBL molfiles 1 or 0 0 (Use ChEMBL molfile coordinates)
engine Chemical toolkit used to generate image RDKit or indigo RDKit

We hope you find these image  rendering changes useful and if you have any questions please let us know via mail to "chembl-help at ebi.ac.uk" if you have any questions.

The ChEMBL Team


Labels:

Comments

Unknown said…
Cool. And what is now the default rendering engine?
23 October 2013 at 07:44
Mark Davies said…
The default rendering engine for the Web Services running off the https://www.ebi.ac.uk/chemblws2 base URL is RDKit
23 October 2013 at 09:15
Post a Comment

Popular posts from this blog

Here's a nice Christmas gift - ChEMBL 35 is out!

By
Use your well-deserved Christmas holidays to spend time with your loved ones and explore the new release of ChEMBL 35!            This fresh release comes with a wealth of new data sets and some new data sources as well. Examples include a total of 14 datasets deposited by by the ASAP ( AI-driven Structure-enabled Antiviral Platform) project, a new NTD data se t by Aberystwyth University on anti-schistosome activity, nine new chemical probe data sets, and seven new data sets for the Chemogenomic library of the EUbOPEN project. We also inlcuded a few new fields that do impr ove the provenance and FAIRness of the data we host in ChEMBL:  1) A CONTACT field has been added to the DOCs table which should contain a contact profile of someone willing to be contacted about details of the dataset (ideally an ORCID ID; up to 3 contacts can be provided). 2) In an effort to provide more detailed information about the source of a deposited dat...
Post a Comment
Read more

Improvements in SureChEMBL's chemistry search and adoption of RDKit

By Eloy
    Dear SureChEMBL users, If you frequently rely on our "chemistry search" feature, today brings great news! We’ve recently implemented a major update that makes your search experience faster than ever. What's New? Last week, we upgraded our structure search engine by aligning it with the core code base used in ChEMBL . This update allows SureChEMBL to leverage our FPSim2 Python package , returning results in approximately one second. The similarity search relies on 256-bit RDKit -calculated ECFP4 fingerprints, and a single instance requires approximately 1 GB of RAM to run. SureChEMBL’s FPSim2 file is not currently available for download, but we are considering generating it periodicaly and have created it once for you to try in Google Colab ! For substructure searches, we now also use an RDKit -based solution via SubstructLibrary , which returns results several times faster than our previous implementation. Additionally, structure search results are now sorted by...
Post a Comment
Read more

ChEMBL 34 is out!

By
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 ...
Post a Comment
Read more

Improved querying for SureChEMBL

By
    Dear SureChEMBL users, Earlier this year we ran a survey to identify what you, the users, would like to see next in SureChEMBL. Thank you for offering your feedback! This gave us the opportunity to have some interesting discussions both internally and externally. While we can't publicly reveal precisely our plans for the coming months (everything will be delivered at the right time), we can at least say that improving the compound structure extraction quality is a priority. Unfortunately, the change won't happen overnight as reprocessing 167 millions patents takes a while. However, the good news is that the new generation of optical chemical structure recognition shows good performance, even for patent images! We hope we can share our results with you soon. So in the meantime, what are we doing? You may have noticed a few changes on the SureChEMBL main page. No more "Beta" flag since we consider the system to be stable enough (it does not mean that you will never ...
Post a Comment
Read more

ChEMBL brings drug bioactivity data to the Protein Data Bank in Europe

By
In the quest to develop new drugs, understanding the 3D structure of molecules is crucial. Resources like the Protein Data Bank in Europe (PDBe) and the Cambridge Structural Database (CSD) provide these 3D blueprints for many biological molecules. However, researchers also need to know how these molecules interact with their biological target – their bioactivity. ChEMBL is a treasure trove of bioactivity data for countless drug-like molecules. It tells us how strongly a molecule binds to a target, how it affects a biological process, and even how it might be metabolized. But here's the catch: while ChEMBL provides extensive information on a molecule's activity and cross references to other data sources, it doesn't always tell us if a 3D structure is available for a specific drug-target complex. This can be a roadblock for researchers who need that structural information to design effective drugs. Therefore, connecting ChEMBL data with resources like PDBe and CSD is essen...
Post a Comment
Read more