We have faced for some time some issues with compound integration with ChEMBL - specifically the loading of compound sets into ChEMBL for cross referencing, between for example, ChEBI, PDBe compounds, etc. The ChEMBL update cycle is relatively slow with respect to some other resources, and there is inevitable thrash with compounds not being present, especially for exciting new data. Without doing something different for compound integration, we were starting to face a scenario where we had a compound table with many millions of compounds without any bioactivity data, and following this the inevitable slowdown in searching, etc.
We also had some issues facing us about curation of other people's primary data, changing compound structures, or their rendering, etc.
So, we decided to set up an external system to resolve cross-references between various databases. This is a very simple Standard InChI lookup, containing compounds from resources such as ChEMBL, ChEBI, PDBe, DrugBank, KEG…
We have made a couple of minor updates to the ChEMBL widgets, which include:
A new widget has been created, which displays the bioactivity results shared between a ChEMBL compound and a ChEMBL targetA new scaling parameter allows you to vary the size of the widgetA more informative message is provided when widget has no data to display
More details can be found here
We're delighted to announce the availability of three distinct new datasets on the ChEMBL-NTD portal, available for download, reuse, etc.
These are: Novartis-GNF Malaria Liver Stage dataset (associated with this Science publication) (Plasmodiumfalciparum).DNDi Human African Trypanosomiasis (HAT) dataset (Trypanosoma brucei)DNDi Chagas Dataset (Trypanosoma cruzi).
Further details of the assays and compounds are to be found on the ChEMBL-NTD portal. The data will be integrated and loaded into a future version of ChEMBL, as well as the direct data download links. Once more, we thanks the depositors, DNDi and Novartis-GNF, for their benevolence and commitment to Open Science.
The associated publication for the Novartis-GNF dataset is:
%T Imaging of Plasmodium Liver Stages to Drive Next-Generation Antimalarial Drug Discovery
%A S. Meister
%A D.M. Plouffe
%A K.L. Kuhen
%A G.M.C. Bonamy
%A T. Wu
%A S.W. Barnes
%A S.E. Bopp
%A R. Borboa
%A A.T. Bright
%A J. Che
%A S. Cohen
%A N.V. Dhari…
On November 18, the FDA approved asparaginase from Erwinia chrysanthemi for the treatment of patient with acute lymphoblastic leukemia (ALL) who have become allergic to the E. coli asparaginase that is conventionally used for the treatment of ALL patients.
ALL is a cancer of the white blood cells and can be fatal within weeks from the onset of the disease if it is left untreated. In ALL, there is an unproportional increase in the population of immature white blood cells, which crowd out functional immune cells as well as red blood cells and platelets, and in advanced stages of the disease infiltrate into tissues and organs, most frequently liver, spleen and lymph nodes. The symptoms of ALL in its initial stages are fatigue, anemia, frequent infections and fever as well as breathlessness and prolonged bleeding. ALL is caused by DNA damage and associated with exposure to radiation and cancerogenic chemicals. There are a number of typical chromosomal translocations, the…
On November 18th 2011, the FDA approved Aflibercept (trade name: Eylea; Research Code: AVE-0005, also known as VEGF Trap), a recombinant fusion protein indicated for the treatment of patients with neovascular (wet) age-related macular degeneration (AMD).
On November 16th 2011, the FDA approved ruxolitinib phosphate (Tradename:Jakafi™ Research Code: INCB-018424), a JAK1/JAK2 inhibitor for the treatment of patients with intermediate or high-risk myelofibrosis, including primary myelofibrosis, post-polycythemia vera myelofibrosis and post-essential thrombocythemia myelofibrosis.
Myelofibrosis is a disorder of the bone marrow, in which the marrow is replaced by scar (fibrous) tissue. Scarring of the bone marrow reduces its ability to blood cells, and can lead to anemia, bleeding problems, and a higher risk of infections due to reduced white blood cells. It is also associated with engorgement of organs suchs as the spleen and liver. Primary myelofibrosis may develop to secondary myelofibrosis - including leukemia and lymphoma. Myelofibrosis is associated with dysregulated Janus kinases JAK1 and JAK2, and some with a somatic mutation in JAK2 (JAK2V617F) (OMIM). JAK signaling involves recruitment of S…
Here is an interesting graph, it the the frequency distribution of the functional PFAM domains for the human ADMET system - more specifically, it is the distribution of domain frequencies for the single domain containing proteins (the multidomain set is being curated now). The source data comes from the PharmADME site (the graph includes the "extended set").
So just 10 distinct functional domains cover almost 75% of the domains (there are a total of 46 domains in this set). By far the most frequent domain is, unsurprisingly, the cytochrome p450 domain (PF00067).
The deadline is approaching for two posts in the ChEMBL group - one a web developer, and the other a data integration position. The posts are three year fixed term contracts. Closing dates for applications is the 27th November 2011.
What options are there for a MySQL Chemical Structure Cartridge ? - the constraints are that the license needs to be Open (to commercial and non-commercial users). Post away in the comments, then everyone can see the answers.
Update: for a little background on our specific interests - we wish to build a deployable and distributable version (a package or vm) with a preconfigured and loaded current ChEMBL database, capable of performing full chemical search capability. Deployment could be as a Linux style package, or as an Amazon EC2 instance. Our internal systems here at the EBI are based on Oracle, and the MDL (or whatever the current name is :) ) Direct cartridge - this configuration is sometimes beyond the reach of many budgets, and so we are interested in exploring a 'free' but useful version of ChEMBL.
Update 2: So Postgres opens up quite a few more options....
In responses to a question from one of the ChEMBL-og readers - I've just checked, and it is possible for non-UK residents to donate to the EBI Movember team - The Bioinformoustachians. Link for donations is above.
Sorry if these posts are a little off normal topic. But the majority of the member of the EBI's team for Movember assembled yesterday for a 'before' photo. Just look at all those baby faces, look at all those chins!