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Showing posts from August, 2014

SureChEMBL Update 1

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.

SureChEMBL Coming Very Soon

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 SureChEMBL UI. A summary of the ch…

Citing ChEMBL, and Data DOIs

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. Kr├╝ger, 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, G. Papadatos, F. Atkinson and J.P…

Registry numbers in ChEMBL

The numbers are in - the public vote (N=69, so quite small) was overwhelmingly (in roughly a 3:1 ratio) in favour of including registry numbers in ChEMBL/UniChem, as you will see from the screenshot above. There was some discussion (see Google+ and ChEMBL-og comments for details, as well as some Twitter response (it's pretty easy to hunt down if you are really really interested). So we will see what we can do.....

ChEMBL US Tour - an update

We've had a great response to our call for offers of venues to help us on a ChEMBL outreach tour, funded by the SMSDrug.net project. Things are shaping up pretty well, but we probably still have space for something in the Seattle area, and also space maybe for something in Philadelphia. We also will probably do both East and West coasts on the same trip, due to the very positive response.
Get in touch if you are in the north-west, or north-east!
jpo

ChEMBL US Tour 2014

We have some specific funding to do some training and outreach for ChEMBL (including UniChem and SureChEMBL). We would like to set something up on either the East or West coasts - the map above is the Google Analytics view for the blog (remember, we don’t run any analytics on the ChEMBL site, we respect your privacy). Based on this there are a couple of realistic options, and we can realistically only do one of these this year. West Coast - Seattle, Bay Area and San Diego.    orEast Coast - RTP, DC, Philly, New York, New Jersey and Boston.
We are thinking of sometime in November or early December 2014.
In order to make this work, we would need a local coordinator to arrange rooms, advertising to local interested users, and so forth, and also some assistance with logistics planning, and if you have access to special rates at hotels that would be great.
We could run either a lecture/chalk-and-talk set of lectures at each location, or if you have a training room with computers could do some …

Should CAS numbers be in ChEMBL and/or UniChem?

A very quick survey to add excitement to either your holiday or work-day! None of these sucker links, where there appears a 0.24% complete progress bar on the second page, it's just a simple yes/no question on whether it's a good idea to add CAS registry numbers to ChEMBL and/or UniChem. No promises that we could deliver this, but depending on what you vote for, we will consider our options.

Update: Given the multiple channels out there, there are also comments on this on LinkedIn (in the ChUG - "ChEMBL User Group" group - why not join, if you're not already) and a couple on Google+.

Update 2: I'll let the poll run till the end of the week (Friday 8th 2014) - and then write something up on the results.