Improved querying for SureChEMBL

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 experience any problem!). In addition, we have introduced two new buttons under the search field. Now it is the time to explain what they do:

Patents with small molecules

If you are using SureChEMBL, it's likely that you are looking for small molecules. However, the database contains millions of patents applying to completely different innovation fields (BTW did you know that Apple recently got a patent granted about sleep tracking?). Though it is difficult to imagine that a search for a specific compound class or a protein target will return the patents about the latest iPhone, there is no guarantee that a patent that matches the right keywords also contains small molecule information. For this reason, we introduced a new filter named "Patents with small molecules". This filter makes use of the IPC/CPC classifications and is derived from the work of Falaguera and Mestres. (2021). More detail on the codes that were used is available in the SureChEMBL Wiki.

Query assistant

Next, we want to introduce the query assistant. If you are not familiar with SureChEMBL, you might struggle knowing where to start with writing your queries. A quick reminder that our Wiki already explains how to write a query using the Solr index, but we can all agree that querying SureChEMBL should be easier. With this idea in mind we developed the query assistant. For those of us familiar with query builders (also called an “Advanced search”), it shouldn't be a break from your usual routine.

Query Assistant in SureChEMBL

Once activated, you simply have to select the fields and the values you want them to take. For instance, select the field 'Title' and enter the value 'cancer' and this will return you with all the patents containing the word 'cancer' within their title. Obviously, you can add more conditions to make your query more precise, and pick a logic operator (AND, OR, NOT). Relatively simple, isn't it?

Obviously it is also limited to linear queries at the moment. For query nesting (e.g. cancer AND pa:(bayer OR novartis OR sanofi)), we ask you to be a bit more patient.

As always, feel free to let us know what you think of these new functionalities, particularly regarding the fields available in the drop down menu of the query assistant. Emails can be sent at surechembl-help@ebi.ac.uk, or you can also directly write an issue in the dedicated GitHub repo.

ChEMBL 15 Year Symposium

Finally, you may have read that we are very soon hosting a symposium at the EBI tomorrow for the ChEMBL 15th and SureChEMBL 10th anniversaries (1st and 2nd October). You can follow the talks on the second day using the link in the agenda here. Hopefully we will see some of you there.

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