The ChEMBL-og

Apparently, there was a huge spike of new granted US patents released by the USPTO a few days ago. The reason? In March 2013, US patent law changed. The ‘first to invent’ became ‘first inventor to file’ for patent protection purposes (see more on this  here ). As a result, a lot of people rushed to submit applications just before the change.  Fast forward 18 months later (last week), a huge spike in USPTO granted patents is observed.  Did SureChEMBL pick that up? See below the cumulative count plot of new patent documents: And the corresponding compound count extracted from these patents: For more information on SureChEMBL, see our previous  posts . George

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 ...

Two new papers from the group have just been published, both in Journal of Chemoinformatics - and of course both Open Access. The first deals with some extensions to UniChem to allow far more flexible searches. The abstract is: UniChem is a low-maintenance, fast and freely available compound identifier mapping service, recently made available on the Internet. Until now, the criterion of molecular equivalence within UniChem has been on the basis of complete identity between Standard InChIs. However, a limitation of this approach is that stereoisomers, isotopes and salts of otherwise identical molecules are not considered as related. Here, we describe how we have exploited the layered structural representation of the Standard InChI to create new functionality within UniChem that integrates these related molecular forms. The service, called ‘Connectivity Search’ allows molecules to be first matched on the basis of complete identity between the connectivity layer of their co...

We got a prize today , so we are happy. What better way to celebrate, than to recruit someone new for the group. We have a position available for a developer to support web service development and integration for the Knowledge Management Centre part of the recently announced NIH Illuminating the Druggable Genome project, see this link for details of the job. Closing deadline for applications is 12th October 2014 .

As announced in the previous SureChEMBL blogpost , the temporary holding page is now in place. So when users visit https://www.surechem.com (or https://open.surechem.com ), you will be redirected to https://www.surechembl.org . For updates on the release of the new SureChEMBL site, please keep an eye on the ChEMBL-og .

In the coming weeks we will be very pleased to announce the release of the new SureChEMBL website. Since the beginning of the year, we have been working hard with the folks over at Digital Science, along with all the content and software providers to get the system setup and running on our own Amazon Web Service controlled environment. As we approach the final stages of the transition, we will need to temporarily halt access to the original SureChem site. The reason for this minor disruption is to allow us to complete the testing of the additional functionality we have added to the SureChEMBL user interface. We will use ChEMBL-og as the primary route of communicating with users, so if you want to be kept up to date, bookmark the site. We will also make ad hoc tweets about SureChEMBL on @johnpoverington, @georgeisyourman, @surechembl and @chembl. SureChEMBL User Interface Users familiar with the previous SureChem UI will find a lot in common with the new...

There are now multiple formats and ways to access the ChEMBL data, and we have recently assigned DOIs to all available versions of ChEMBL (and will archive these on the ftp server, permanently). So when you publish use of ChEMBL, could you reference the following papers: ChEMBL Database A. Gaulton, L. Bellis, J. Chambers, M. Davies, A. Hersey, Y. Light, S. McGlinchey, R. Akhtar, A.P. Bento, B. Al-Lazikani, D. Michalovich, & J.P. Overington (2012) ‘ChEMBL: A Large-scale Bioactivity Database For Chemical Biology and Drug Discovery’ Nucleic Acids Res. Database Issue , 40 D1100-1107. DOI:10.1093/nar/gkr777 PMID:21948594 A.P. Bento, A. Gaulton, A. Hersey, L.J. Bellis, J. Chambers, M. Davies, F.A. Krüger, Y. Light, L. Mak, S. McGlinchey, M. Nowotka, G. Papadatos, R. Santos & J.P. Overington (2014) ‘The ChEMBL bioactivity database: an update’ Nucleic Acids Res . Database Issue , 42 1083-1090. DOI:10.1093/nar/gkt103 PMID: 24214965 myChEMBL R. Ochoa, M. Davies...