ChEMBL Resources

Resources:
ChEMBL
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SureChEMBL
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ChEMBL-NTD
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ChEMBL-Malaria
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The SARfaris: GPCR, Kinase, ADME
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UniChem
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DrugEBIlity
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ECBD

Wednesday, 21 December 2011

Omics and Personalised Healthcare - February 2012


We're speaking at the forthcoming EMBL Conference on Omics and Personalised Healthcare in Heidelberg, held 16th to 18th February 2012. We'll present some of our recent work on pharmacogenetic variation, and some strategies on both data-mining and some of the implications for drug discovery.

Saturday, 17 December 2011

Three ChEMBL talks at the March ACS in San Diego



A number of the ChEMBL team will be at the ACS in San Diego next March - we'll be giving a couple of talks -  one is one drug safety (jpo) one is on peptide SAR analysis and design (Patricia Bento) and the final one is on UniChem (Jon Chambers). So hopefully see you there!

We'll be spending some time in the lab of one of our close collaborators - Mike Gilson at UCSD, but we're happy to meet up with others, give talks, training, etc. as time and travel schedules permit. So if you're interested in this, get in touch.

Update: Fixed post, to reflect three accepted talks.


PAPER ID: 20839
PAPER TITLE: "Drug combinations to reduce adverse drug reactions and improve intrapatient differences in response"
DIVISION: CINF: Division of Chemical Information
SESSION: Systems Chemical Biology and Other 

PAPER ID: 22715
PAPER TITLE: "UniChem: A prototype unified chemical structure cross-referencing and identifier tracking system"
DIVISION: CINF: Division of Chemical Information
SESSION: InChI Symposium

PAPER ID: 15760
PAPER TITLE: "Comprehensive analysis of explored and available physicochemical space for alpha-amino acids"
DIVISION: ORGN: Division of Organic Chemistry
SESSION: Peptides, Proteins, and Amino Acids

Friday, 16 December 2011

Kinase SARfari ver.5.0 Released

We would like to announce the release of new version Kinase SARfari. The latest version has been updated using the chembl_12 data, which contains:

  • Bioactivity datapoints: 503041 (+15%)
  • Compounds: 54189 (+6%) 


 Various dumps of the data from Kinase and GPCR SARfari are also downloadable from the download page.

 Of course, we welcome feedback from our users!

Thursday, 15 December 2011

Spotfire DecisionSite replacement


We used to use Spotfire DecisionSite for data visualisation, and liked it a lot - we've just found out there are some pretty major changes to the licensing; and are now looking for alternatives if we can't work out a way forward. So, any suggestions for good data exploration tools, preferably with some sort of chemistry capabilities. Ideally they would run natively on Mac OsX.

Ideas in the comments please.....

Friday, 9 December 2011

Rough Breakdown of Drug Classes for 2011

Here's the equivalent view of drug approvals for 2011 so far - pretty similar picture in terms of the distribution of molecule classes - but remember this set of drug approvals, got their USANs assigned, on average about 3 to 4 years ago, so the sets are not strictly comparable, and of course, suffer from small absolute numbers....

Wednesday, 7 December 2011

Happy ChEMBLmas!!




As part of our tradition of making Xmas seasonal eCards to all our users - above is the December 2012 card. For the geeky amongst you, there may be an Easter Egg in the image file....

Conference: Advances in Protein-Protein Interaction Analysis and Modulation


Registration is now open for a really interesting EMBO Workshop on the modulation of protein-protein interactions (ppi's). We're speaking, and will present some new stuff on annotation of ChEMBL with interacting domains, and a sort of classification of these into protein-protein interfaces (see some previous blog posts for some further details on this).

The meeting is in the beautiful French harbour town of Roscoff - the traditional home of Onion Johnnies - well, I love onions, and my name is John, and I'll be there!


Tuesday, 6 December 2011

Amgen Scholars Program


Due to a lot of wasted time in the past, my lab does not host or support applications to the Amgen Scholars Program, so please do not apply to us!

Papers: MIRIAM and Identifiers.org


The NAR Database Issue is currently in full flow, and there are many excellent articles; one important one for ChEMBL is this paper from the group of our good friend Nicolas Le Novere, at the EBI. It addresses a really important problem in biological and chemical data integration through the generation of unique and stable identifiers for records in a data collection – these are MIRIAM identifiers (MIRIAM is an acronym for Minimum Information Required in the Annotation of Models Registry (http://www.ebi.ac.uk/miriam). Identifiers.org is a new service (http://identifiers.org) that is built upon the information stored in the MIRIAM Registry and which provides directly resolvable identifiers, in the form of Uniform Resource Locators (URLs). Resources such as this are essential components for ad hoc, distributed queries across disparate data sources, and a core component for semantic web development. 

A link to the free pdf of the paper is here.

ChEMBL is in identifiers.org, give it a go!

%J Nucleic Acids Research
%D 2011
%O doi:10.1093/nar/gkr1097
%T Identifiers.org and MIRIAM Registry: community resources to provide persistent identification
%A N. Juty
%A N. Le Novere
%A C. Laibe

Monday, 5 December 2011

MIPTEC 2012 and EMBO Chemical Biology 2012


A quick post to say that two of the best conferences in Europe next year are coordinating speakers and schedules for the Drug Discovery sessions to allow a really great line-up of talks and speakers, and to allow the best use of your (always too small!) travel budgets for conference attendance in these economically tough times. More later, but pencil both conferences into your diary now!

MIPTEC 2012 - September 24th to 27th 2012, Basel, Switzerland
EMBO Chemical Biology - September 26 to 29th 2012, Heidelberg, Germany.

Saturday, 3 December 2011

Cape Town


I've just spent a great week in Cape Town, at UCT, visiting the lab of Kelly Chibale; where there's lots of activity in academic drug discovery, and also at the Institute of Infectious Disease and Molecular Medicine. My first time in Africa, and it won't be my last!

Friday, 2 December 2011

3,788 Thank yous!

So a big and heart-felt three thousand, seven hundred and eighty eight 'Thank Yous' to all the benevolent donors to the EBI Movember Team - The Bioinformoustachians. It was a lot of fun, the place is a lot hairier now, and there are more smiles on faces than at the start of the month.

Mission accomplished by our International (hair)peace keeping force - The Victoria and George Crosses (respectively) are awarded to Francesco Iorio (sgt. 8th Italian light foot) and Remco Loos (cpl. 4th Dutch commando) for their epic struggle and hand-to-hand combat for first place in the fund-raising league table, and a 'mention in despatches' is presented to Nicolas Le Novére (lt. 1st French prancers) for being the 'Top Gun' amongst the faculty. The platoon is now returning home, and will soon be changing back into 'civvies' (much to the relief of their partners and family).

If any other large science data centres want to make a fight of it for Movember 2012 - bring it on, we are waiting!

PS, it's still not too late to donate (up to December 8th 2011) at http://mobro.co/ebi

Thursday, 1 December 2011

ChEMBL 12 Released

We are pleased to announce the release of ChEMBL_12. This latest version of the ChEMBL database contains:
  • 1,222,969 compound records
  • 1,077,189 distinct compounds
  • 596,122 assays
  • 5,654,847 bioactivities
  • 8,703 targets
  • 43,418 documents
  • 7 data sources
This release includes updates to the manually extracted Medicinal Chemistry literature, a number of published ADMET datasets (for metabolic enzymes and various transporters), updates to OrangeBook drug approvals and a partial update from PubChem BioAssay. ChEMBL_12 also contains a new deposited dataset of Malaria liver-stage screening data from Novartis-GNF (for more details on this dataset, please see ChEMBL-NTD website and the recent publication in Science).

Please refer to the ChEMBL_12 release notes for a more detailed description of all changes included in this release.

You can download the data from the ChEMBL ftpsite: ftp://ftp.ebi.ac.uk/pub/databases/chembl/ChEMBLdb/latest/