ChEMBL Resources

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ChEMBL-Malaria
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The SARfaris: GPCR, Kinase, ADME
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DrugEBIlity
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ECBD

Friday, 19 September 2014

SureChEMBL Available Now





Followers of the ChEMBL group's activities and this blog will be aware of our involvement in the migration of the previously commercially available SureChem chemistry patent system, to a new, free-for-all system, known as SureChEMBL. Today we are very pleased to announce that the migration process is complete and the SureChEMBL website is now online.

SureChEMBL provides the research community with the ability to search the patent literature using Lucene-based keyword queries and, much more importantly, chemistry-based queries. If you are not familiar with SureChEMBL, we recommend you review the content of these earlier blogposts here and here. SureChEMBL is a live system, which is continuously extracting chemical entities from the patent literature. The time it takes for a new chemical in the patent literature to become searchable in the SureChEMBL system is 1-2 days (WO patents can sometimes take a bit longer due to an additional reprocessing step). At time of writing this blogpost the number of unique compounds in SureChEMBL is 15,760,514, which have been extracted from 12,949,021 patents.

To get started using SureChEMBL, head over to the homepage, where you will be presented with a range of search methods and filters. The image below provides a brief overview of the search functionality offered by the system:




To provide an example of how to use the SureChEMBL website, let's assume you are interested in patents which contained structures similar (or identical) to Sildenafil in the claims section of the document and also mention the term PDE5 anywhere in the document. To run this search, go to the SureChEMBL homepage and carry out the following actions:
  1. Enter the term 'PDE5' in the search text box 
  2. Sketch in the structure of Sildenafil (or use the name look-up function)
  3. Change the search type to similarity (>85%) 
  4. Click the 'Claims' checkbox in the document filter section and 
  5. Hit 'Search' button


After clicking 'Search', you will be presented with a page which contains all compounds that match your search criteria:





From the compound results page above you then have the choice of either exporting the chemistry (all the compounds returned by the search) or viewing the patents associated with 1 more of the selected compounds. For the selected compounds in this search, the associated patents (sorted by descending publication date) are :


 

From the patent document results page, you are able to export chemistry from all documents on display, view patent family information and view the chemistry-annotated, full text document. The claims section of the first patent (US-20140255433-A1) includes references to both sildenafil and PDE5:


 

The aim of this blogpost is to introduce the SureChEMBL system and not to provide a comprehensive review of all the functionality the system offers. This will be covered in future training sessions and webinars, which will be announced on this blog in the near future.

We would like to thank the people over at Digital Science, who were responsible for building the original SureChem system and supported its migration over to EMBL-EBI. In particular, we would like to thank Nicko Goncharoff, James Siddle and Richard Koks.

The system runs on the cloud - specifically on Amazon Web Services, a stable, secure and highly scalable way to deploy web applications. We need to keep a close eye on performance and patterns of usage over the coming weeks, to get an idea of how many servers, etc, we need for full deployment. In particular, we will throttle scripted access,  so please get in touch if you want to try anything like this, so you are not frustrated by slow performance, and we will try and accommodate your use case. There is also a download link on the homepage, so please explore this if you are interested.

We have an exciting roadmap for the future development of SureChEMBL, bt if you have any priority requests, mail them to surechembl-help (at) ebi.ac.uk.

If you experience any issues with the system, or have any questions please get in touch.

4 comments:

Christopher Southan said...

Good stuff but pleast try to get the through-link auto searches from PubChem working again. Granted I can paste the SMILES and launch the search but it was nice to have that already executed in the linking

Richard H said...

I think this will be a valuable resource, thanks. I was wondering if it was possible to link from an SCHEMBL identifier (as reported in the downloaded SD file) back into the SureChEMBL website? I couldn't see a way to do this.

Mark Davies said...

Hi Richard,

You can use the following example URL to link back to the SureChEMBL website: https://www.surechembl.org/chemical/SCHEMBL1895

Mark

Richard H said...

Great, I'll give that a whirl, thanks Mark :)