The ChEMBL-og

A couple of us are out in New Orleans for the ACS in a few weeks - if any ChEMBL users would like to meet up to get some training, ask questions, suggest improvements to what we do, or just grab a beer or coffee, we'd be very happy to do so. We arrive Sunday and leave Tuesday night. The picture is rather amusing, and looks a little like Mark and me, sort of. Credit for image is detailed in the image itself..... jpo and mark

There's a paper just out from Samuel, one of the PhD students in the group - the link to the Open Access paper is here .  Brain is a Java software library facilitating the manipulation and creation of ontologies and knowledge bases represented with the Web Ontology Language (OWL). %A S. Croset %A J.P. Overington %A D. Rebholz-Schuhman %D 2013 %T Brain: Biomedical Knowledge Manipulation %J Bioinformatics %V 29 %O DOI:10.1093/bioinformatics/btt109 %O PMID:23505292

ATC Code: Not Assigned Wikipedia: Ospemifene On February 26, FDA approved Ospemifene ( Trade Name : OSPHENA ,  PubChem :  CID 3036505 ,  ChEMBL :  CHEMBL210 5395 , ChemSpider :  2300501 ) for the treatment of moderate to severe Dyspareunia  - symptom of vulvular and vaginal atrophy due to menopause. Dyspareunia , is pain during or after sexual intercourse. It can affect men, but is significantly more common in women, affecting up to one-fifth of women at some point in their lives. Women with dyspareunia may have pain in the vagina, clitoris or labia. This may be due to medical or psychological causes. There are numerous medical causes of Dyspareunia, like : Vaginismus , Pelvic Inflammatory Disease , Genital or Pelvic Tumors, Urethritis , Urinary Tract Infection , Vaginal Atrophy , Vaginal Dryness , Vulvar Cancer , Childbirth Trauma (postpartum), Skin Conditions (Lichen Sclerosus, Lichen Planus, Eczema, Psoriasis), Female ...

A few weeks ago we ran a small poll on how we should deal with inorganic molecules - not just simple sodium salts, but things like organoplatinums, and other compounds with dative bonds, unusual electronic states, etc . The results from you were clear, there was little interest in having a lot of our curation time spent on these. We will continue to collect structures from the source journals, and they will be in the full database, but we won't try and curate the structures, or display them in the interface. They will be appropriately flagged, and nothing will get lost. So there it is, democracy in action. So for ChEMBL 16 expect fewer issues when you try and load our structures in your own pipelines and systems. Thanks for all your input. jpo

We are partners in the diXa FP7 infrastructure grant for chemical safety 'omics data, and as part of this, there is a course aimed at people who could benefit from an introduction to microarray data analysis. This will take place at the EMBL- EBI from 14 -16 May 2013 . No prior R or Bioconductor experience is required. Registration closes on 21 st April 2013 . This course is aimed at researchers and scientists (PhD students, post-doc, staff scientist) who will benefit from an introduction to microarray data analysis and training in how to perform simple analyses using R/Bioconductor. All sessions are a combination of lectures and hands-on. Prerequisites are a life science degree or equivalent experience, basic understanding of microarray techniques, and a basic understanding of biostatistics. No prior knowledge of R or Bioconductor is assumed. Participants will receive a basic understanding of the R syntax and ability to manipulate R objects. After this...

Here's a little tip that may be of some use to you. The compound name search feature will also match substrings, so it is easy to type in a USAN/INN stem, and then retrieve all matching compounds - for example, "gliptin" will retrieve all DPP-IV inhibitors with non-proprietary (formal) names. This is pretty useful - of course the substring search functionality is not restricted to USANs/INNs. A list of the current USAN stems is here . Note, they were never designed to be orthogonal, so the low complexity ones will give a lot of false positives.....

One of our Industry Programme members passed on a listing for some positions they are looking to fill at the new center in Heidelberg - BioMed X. It looks like it may be of interest to many of the ChEMBL-og readers, so I thought I would post it here.... They are looking for a Computational Chemistry/Drug Design group leader for a project "Development of a design software of SELECTIVE kinase inhibitors". The BioMed X Innovation Center in Heidelberg, Germany, constitutes a new class of incubator at the interface between academia and industry where top life science talents from all over the world are jointly working on biomedical innovation outside the pharma box. Young talents from leading academic institutions world-wide are selected in annual assessment centers based on their scientific expertise, creative energy, and passion for product-oriented pre-clinical research & development. Interdisciplinary project teams are collaborating in an open-innovation lab facility in...