• ChEMBL_09 BioTorrents Available

    The flat files (sdf, chemical representatives, fasta and release notes) and the mysql dump from the latest ChEMBL release are now available as torrents on the BioTorrents website, click here for more details. We have been a bit slack in maintaining the ChEMBL BioTorrent downloads, but will always aim to make the these torrent files available for future ChEMBL releases.

  • Beautiful map of scientific collaborations


    I came across this map of scientific collaborations on Twitter - really interesting. Full details here.

  • Be Afraid of Spam Filters


    I am ill, in bed, taking paracetamol and caffeine. I can still type though, but am bored...

    I had an email problem recently where people appeared to be ignoring my mails, simple things that would have taken a moment to think about and reply to. When asked, they nonchalantly replied they never got it, and I thought I was going mad. However, the messages were in my Sent mail folder, and on checking, found that they never arrived at the recipients mailbox. I mailed the systems team with a copy of the failed delivery messages, and no reply (they failed to be delivered also). Messing around with test mails established a phenotype for failure - guaranteed to fail were messaged with an image, a url and a drug name. Various cut down versions (e.g. no image, but a drug name and a web link) may or may not have failed, depending on the precise message. After the penny dropped, the problem was with our internal spam filter, holding my mail in quarantine, silently, for ever. Of course, part of my job is to make frequent drug references, so there is some irony in this for me.

    So, bottom line is that it is remarkably easy to trigger mail server spam filters with technical discussion of drugs. My local fix was to be whitelisted for internal mail - I can now send all sorts of spam, with complete impunity (trust me, I have tested it). So if anyone else has a similar problem and needs to refer to drugs as part of their work, maybe this post may just help (assuming the ChEMBL-og is not blacklisted...)

  • Chembl_09 Schema - A Different View


    The guys at the NCI Cactus blog have done a great job of rendering the new ChEMBL schema as released in ChEMBL_09. There are quite a few changes, and we have started to load/curate new data against this schema - so check with us if your analyses rely on something currently in there! Click on the above image for a large view.

    Things will be fairly quiet at ChEMBL Manor next week - we have the annual ChEMBL training course which will keep us busy, and hopefully out of any trouble.

  • February 2011 USANs


    The February 2011 USANs have been published, these are:



    USAN
    Research code
    Structure
    Drug Type
    Drug Class
    Target
    BIBW-2992
    synthetic small molecule
    therapeutic
    AGN-210937
    synthetic small molecule
    therapeutic
    		EP2 receptor
    AGN-212409
    synthetic small molecule
    therapeutic (prodrug)
    		EP2 receptor
    AGN-210961
    synthetic small molecule
    therapeutic (prodrug)
    Bavisant Bavisant dihydrochlorideJNJ-31001074synthetic small moleculetherapeuticH3 receptor
    Lesinurad sodiumRDEA-594
    		synthetic small moleculetherapeuticURAT1
    OxelumabRO-4989991 R-4930 huMAb-OX40L





    		monoclonal antibodytherapeuticCD252
    VemurafenibPLX-4032, RO-518426, RG-7204synthetic small moleculetherapeuticMEK RAF1 BRAF





    Drug Type
    Number
    synthetic small molecule
    8
    natural product derived small molecule
    0
    protein
    1
    monoclonal antibody
    1
    enzyme
    0
    Cumulative total for 2011
    10

  • EMBL-EBI Open Day March 2011


    Registration is now open for the next EMBL-European Bioinformatics Institute Open Day, which will take place on Tuesday 15th March 2011.

    The 'Open Day' is the perfect opportunity for young scientists who are considering a career in bioinformatics (and related disciplines) to find out more about opportunities at Europe's main centre for bioinformatics. You will learn about cutting-edge research projects, get an overview of one of the world's most important collections of biological databases and tools, and be given time to talk one-to-one with the experts who develop and curate these services. There is also the chance to hear a talk from one of the ChEMBL team, talking about a curator job.

    Registration is FREE, but places are limited to 40 so please register now to avoid disappointment. Please go to http://www.ebi.ac.uk/training/openday/ for a full programme and registration details.

  • Ideas for Holidays?


    There is a cool travel guide (cool if you are a nerdy scientist, I am!) available on the website of the British Society for the History of Science (BSHS). Don't worry, it doesn't just deal with staycations, but with interesting places around the whole world.

  • ChEMBL_09 released


    We are pleased to announce the release of ChEMBL_09 and a new version of the ChEMBL web interface. This release of the ChEMBL database contains initial entries for small molecule and biotherapeutic drugs, together with product information from the FDA Orange Book. This data will be subject to further updates and curation in subsequent releases and therefore some property assignments should be considered preliminary. It should also be noted that a number of the approved products do not have therapeutic uses (e.g., diagnostic agents, additives etc.). These non-therapeutics are currently included in the database, but are flagged as such. We have also now incorporated the chemical structures of ligands from entries in PDBe (Protein Data Bank in Europe) into to ChEMBL.

    Use of ChEBI IDs: ChEMBL will continue to assign ChEBI identifiers to small molecules with known structures, and these compounds will be indexed by ChEBI for search purposes. However, only a subset of highly curated entries will be displayed on the ChEBI web-interface or provided in their downloads. ChEMBL compounds are also now deposited directly into PubChem.


    Schema Changes: There are significant schema changes this release, to allow the incorporation of the approved drug data. Please see release notes for more details.

      Interface Enhancements:
    1. 'Browse Drugs' tab, which allows users to view, search and download the drug data stored in ChEMBL database (https://www.ebi.ac.uk/chembldb/index.php/drugstore)
    2. A new Document report card page has been created, which summaries target, activity, compound and assay data found in a ChEMBL journal article. All previous links to PUBMED now go to this page (e.g. https://www.ebi.ac.uk/chembldb/index.php/doc/inspect/CHEMBL1153406)
    3. Only parent compound structures are returned in the compound searches
    4. Bioactivity results display both parent and salt/ingredient structures
    5. Compound report cards updated to include a Clinical Trials and Molecular Forms sections (e.g. https://www.ebi.ac.uk/chembldb/index.php/compound/inspect/CHEMBL941)
    6. A choose of 3 compound sketchers (JME, Marvin, JDraw) are now available on compound search page
    7. Japanese translation of home page