The ChEMBL-og

For the last three months, I've been busy working my way through a 9000 long (sometimes headache-inducing) set of ChEMBL compound ids. These had been highlighted for curation for the reason that for each ChEMBL_id in the list, there were two or more compound keys from the same paper. This implied that either there were two indistinguishable using InChI representation compounds described in the paper or they were different compounds that had been somehow merged together in the database. Each ChEMBL_id was individually checked against the data in the original paper to see if there were indeed two compound keys for the same structure. The outcome of this check gave rise to one of four cases: The structure(s) was found to be incorrect and was redrawn. The structure was correct for some records but not others, so a new compound was created for those selected records. The structure required the definition of stereochemistry or a salt. The structure was le...

ATC Code: L04A (partial) Wikipedia: Pomalidomide On February 8 th , the FDA approved Pomalidomide (Tradename: Pomalyst ; Research Code: CC-4047, IMiD 3), a thalidomide analogue, indicated for the treatment of multiple myeloma in patients who failed to respond to previous therapies (e.g. lenalidomide and bortezomib ). Multiple myeloma is a form of blood cancer that primarily affects older adults, and arises from the accumulation of abnormal plasma cells in the bone marrow. These abnormal plasma cells produce large amounts of unneeded antibodies, which are then deposited in various organs, causing renal failure, polyneuropathy and other myeloma-associated symptoms. Pomalidomide, an analogue of thalidomide, is an immunomodulatory agent with antineoplastic activity. Like other thalidomide analogs, the exact mechanism of action is yet not fully understood, however in vitro assays demonstrated that pomalidomide inhibited proliferation and induced apoptosis of hematopoietic ...

We'll be organising the 2nd RDKit Users Group Meeting which will be held from the 2nd until  the 4th of October 2013 here at the EMBL-EBI in Hinxton. In addition to  two days of talks, tutorials and  discussions, the last day  will be dedicated to a coding/documentation sprint. Stay tuned for more information, as well as a call for presenters, which will come over the  next few weeks, but, in the meantime, please go ahead and block the dates in your  busy calendars! George

A couple of weeks ago, I created a Doodle Poll to gauge interest in  hosting another series of Webinars, after the success of the ones we hosted last year. After a good response, these Webinars have now been organised and those who are interested in signing up to them, can do so here . Most of the webinars will only take 45mins and will give a good overview of the topic that they are talking about. You can watch and listen to them from the comfort of your own desk. The Doodle Poll signup section is hidden so only us here at ChEMBL Towers can see your personal details. However, I must stress that it is important that you leave your name and email address on the poll when you sign up, so that I can send on the connection details for the Webinar. Without this information, you will not be able to take part as I won't know where to send the connection details to. Any issues or queries, please do not hesitate to contact ChEMBL Help .

For the recent ChEMBL_15 release, a considerable part of our efforts was focussed on the standardisation and harmonisation of the data in the Activities table. The latter holds all the quantitative and qualitative experimental measurements across compounds, assays and targets; needless to say that without it there's no ChEMBL ! This is a summary of what we've incorporated so far: Flag missing data: Records with null published values and null activity comments were flagged as missing. Standardise activity types and units: Conversion of heterogenous published activity type descriptions and units to a standard_type and set of standard_units (e.g., for IC50 convert mM/uM/pM measurements to nM). Flag unusual units: Records with unusual published units for their respective activity types were flagged as 'non standard'. For example, a hypothetical record with IC50 type and units in kg would be flagged! Convert the log values: The records with activity types ...

ATC Code: C10AX11 Wikipedia: Mipomersen On January 29 st , the FDA approved Mipomersen (Tradename: Kynamro ; Research Code: ISIS-310312), an oligonucleotide inhibitor of apolipoprotein B-100 (apo B-100) synthesis, indicated as an adjunct to lipid-lowering medications and diet to reduce low density lipoprotein-cholesterol (LDL-C) , apolipoprotein B (apo B), total cholesterol (TC) , and non-high density lipoprotein-cholesterol (non HDL-C) in patients with homozygous familial hypercholesterolemia (HoFH) . Familial hypercholesterolemia is a genetic disorder, characterised by high levels of cholesterol rich low-density lipoproteins (LDL-C) in the blood. This genetic condition is generally attributed to a faulty mutation in the LDL receptor (LDLR) gene, which mediates the endocytosis of LDL-C. Mipomersen is the first antisense oligonucleotide that targets messenger RNA (mRNA) enconding apolipoprotein B-100 (Apo B-100), the principal apolipoprotein of LDL and its metabolic pre...

After the success of the last round of webinars , we have decided to run another set. However, we would like to gauge the interest in which topics would be most useful. The topics that have been suggested so far are: ChEMBL Overview - Basic interface walkthrough and searching ChEMBL Schema - Basic overview and ChEMBL changes ChEMBL Schema - Changes to ChEMBL target data model UniChem - Basic overview and searching Drug and USAN data content For this, a doodle poll has been set up which will allow you to register your interest. The poll is hidden, so no one will see your details, but it will allow us at ChEMBL Towers to see if the webinar would be worthwhile to set up. Please click on the link and let us know what you think. Additionally, if there are any webinars that we have not suggested, that you believe would be useful, please feel free to suggest these on the doodle poll, or email chembl-help@ebi.ac.uk