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Thursday, 19 December 2019

Merry Christmas and ChEMBL_26 coming soon!


The ChEMBL team will be heading off for Christmas soon, but just before we do, we wanted to share some updates...

First, thanks to all of our many users and collaborators and we wish you all a happy holiday season and a productive 2020!

Thanks also to everyone who helped us celebrate 10 years of ChEMBL at our symposium in October. For those who were unable to make it on the day, many of the talks and posters are available here.

Over the last few months we've been busy working on ChEMBL_26, which we plan to release early next year. There will be some important changes in this release:

We are now using RDKit for almost all of our compound-related processing. For the first time in ChEMBL_26, this will include compound standardisation (look out for more info on this in the new year), salt-stripping, generation of canonical smiles, structural alerts, substructure searches and similarity searches (via FPSim2). Therefore, all molecules have been reprocessed and you may notice some differences compared with previous releases.

We have also switched our pKa calculations to use ChemAxon software. The compound properties ACD_MOST_APKA, ACD_MOST_BPKA, ACD_LOGP and ACD_LOGD will now therefore become CX_MOST_APKA, CX_MOST_BPKA, CX_LOGP and CX_LOGD.

Target predictions are also now being generated by a new method, using conformal prediction models.

Finally, our old ChEMBL interface will be switched off at the end of the year, so if you haven't made the jump yet, now is the time! We are still making improvements to the new interface and adding new features, so if you have any suggestions or feedback please do let us know.


The ChEMBL Team


Friday, 13 December 2019

Mechanism of Action and Drug Indication data on the interface.

Two new 'Browse' pages have been added to the interface; Browse Drug Mechanisms and Browse Drug Indications. Users can now access these 2 pages directly to explore all the data. Or alternatively, they can land on these pages from drugs, compounds and targets in ChEMBL.

Accessing all the data from the main page


The 'circles' visualisation on the main page shows a summary of the entities in ChEMBL. Circles for Drug Mechanisms of Action and Drug Indications have been added. By clicking on the circles, you will be taken to a page that allows you to explore the corresponding entity. 
Visualisation that summarises the entities in ChEMBL, Drug Mechanisms of Action and Drug Indications are now included.

The Browse Drug Mechanisms and Browse Drug Indications pages allow you to use filters, link to other entities, and download the data in the same way as the other 'Browse' pages.

All Drug Mechanism data.
All Drug Indication data.

Accessing Drug Indication and Drug Mechanism data related to other entities


You can now explore the Drug Indication and Drug Mechanism data in relation to the following entities:

From Browse Drug Mechanisms you can:
  • Browse related Drugs
  • Browse related Compounds
  • Browse related Targets

From Browse Drug Indications you can:
  • Browse related Drugs
  • Browse related Compounds

From Browse Drugs you can:
  • Browse related Drug Mechanisms
  • Browse related Drug Indications
  • Browse related Activities

Example A:


1. Go to the Browse Drug Mechanisms page. Find all drugs with mechanisms as neurokinin receptor antagonists.
Note that the data describes the mechanisms of action of 17 compounds for 3 targets.



2. Select all items and click on 'Browse Drugs', a new tab will open showing the drugs for the targets selected in step 1.



3. Click on 'Browse Drug Indications' to view all annotated indications for the drugs in step 2.




Example B:


1. Go to the Browse Drug Indications page. Find all drugs whose indication is asthma. There are 175 entries with asthma as an indication.



2. Select all items and click on 'Browse Drugs', a new tab will open showing the drugs for the indications selected in step 1.




3. Click on 'Browse Drug Mechanisms' to view of all annotated mechanisms for the drugs in step 2.



Accessing Drug Indication and Drug Mechanism data from report cards

You can now go to a dedicated page from the Drug Mechanism and Drug Indication data in the report cards. For example go to the report card for IMATINIB (CHEMBL941)

https://www.ebi.ac.uk/chembl/compound_report_card/CHEMBL941/

In the Drug Mechanism section you can see the data for that compound. If you click on 'Browse All', you will be directed to the Browse Drug Mechanisms page showing the data.

Drug Mechanisms section for the report card of IMATINIB (CHEMBL941)

Similarly, in the Drug Indications section you can click on 'Browse All' to be directed to a 'Browse Drug Indications' page showing all the data.
Drug Indications section for the report card of IMATINIB (CHEMBL941)


If you have any questions, please contact the ChEMBL Team support (chembl-help [at] ebi.ac.uk)