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Bio <-> Chem

Technical notes from the interface between bioinformatics and cheminformatics by Chris Southan
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AstraZenecaCode NumbersOpen InnovationRepurposingBiological Sciences
Published
Author Christopher Southan

Update : the resolved structure mappings below have been loaded into the latest release of GtoPdb. They can be retrieved with the query AZD* Open innovation has a somewhat elastic definition.

PatentsBiological Sciences
Published
Author Christopher Southan

Back at the beginning of the year I accepted a invitation for commentary that duly appeared in "Patent analytics: current tools and emerging trends" with an eminent set of co-authors (paywalled and PubMed indexed but without author names) However,  I was chagrined to find that when I got the proofs back only about 50% of the 2000 words I had submitted were included in with the other comments.

Biological Sciences
Published
Author Christopher Southan

Updates :  LCZ696 made FDA approval for heart failure as Entresto in July 2015 and received a recommendation for EU approval in Sept 2015. ****************************************************************************** Update 2nd Sep.  Nice to gets a cross-pointer from today's  In the Pipeline post on the same subject.

BioDrug RepurposingPatentsBiological Sciences
Published
Author Christopher Southan

22 Aug, see new external contributions at the end of this post. OK, so lets go database ferreting again (def. bring to light by searching) - with the latest batch of  NCATS Industry-Provided Agents  for repurposing.

AntimalarialsBioPatentsBiological Sciences
Published
Author Christopher Southan

Update: 25 July. Nice to be selected for ACS SciMix poster so I have compiled CID list at bottom of post that included a few new CIDs. Update: 1st July . New video on DSM265 story (no. 6 below). Note also t he recent post on entity resolution for the antimalarial review includes many of compounds in this list. Update: 17th June 2015.

ChemChEMBLDrugBankDrugsPubChemBiological Sciences
Published
Author Christopher Southan

As an introduction to this important subject I can point to our abstract and poster from BioIT 2014 (since superseded by an updated version) Reading the poster is optional of course but I'll minimise the preamble to this post assuming you have.  In addition there is a new blog post over at GToPdb  that outlines how we have used consensus drug CID lists as curatorial starting points for the latest release.

BioChemText MiningBiological Sciences
Published
Author Christopher Southan

Update 20th June. Thanks to all those involved from the Faculty and BioIT side, the workshop was a success, evidenced by complimentary feedback.   It took a while to get to "quorum" in the sign up phase but this was simply because we were competing against many other good offerings on that day. The attendees should have had links to the slide sets.

BioClinical TrialsBiological Sciences
Published
Author Christopher Southan

Around the 30th of Jan twitter was echoing with the phrase “Stunning Win For Open Science” as the headline announcement that Johnson & Johnson was going to release (via Yale as an intermediary)  clinical trial data to researchers which even made it to the New York Times. This not only gave me a déjà vu feeling from the GSK announcement but I also recalled the three  J&Js we looked at in the  NCATS/AZMRC