Conference: Bioinformatics for Anti-Cancer Drug Discovery

There is a conference that we are presenting some new ChEMBL work and analysis at, and also there is a talk on CanSAR. The conference is at Bilkent University, in Ankara, Turkey. Dates are fairly soon though  - 17th and 18th October 2011, but there is still time to submit an abstract - I wish more conferences were like this, in not having a big gap between the conference and any deadlines for submission.

The conference website is http://www.i-cancer.org/bioinformatics2011.

As an aside, I hadn't linked Ankara in Turkey before to the word Angora (Angora is an old name for Ankara), so this is the place responsible for the Angora goat, rabbit and cat!

Lipinski Seminar - Cancelled

Unfortunately Chris has cancelled his entire UK trip next week, due to a patent case being heard in the States that he is involved with. Subsequently his seminar on campus next week is also cancelled.

Recruitment - Data Warehouse Developers for a new grant

We have recently completed the legal formalities for an exciting collaborative grant involving the development of a service infrastructure for data from EU-funded research into non-animal tests for predicting chemical safety. - the grant is called DiXa. We are currently recruiting two positions for this grant (and there will be some additional posts later). These will be in the group of Ugis Sarkans at the EBI.

Further details on the positions can be found here.

• Post 1
• Post 2

Antibody Drugs in Development

There are a large number of antibody drugs in development - there are about 580 in the current ChEMBL list (click here for Excel spreadsheet). I've stripped out some of the fields for clarity, but it should be pretty obvious what everything is.

So, given that we'll start loading our biological drug sets into ChEMBL shortly, is there any key data missing, as always, any feedback on errors, etc would be greatly appreciated. If anyone would like a file of all the sequences that we have, let me know.

A couple of notes on the data content

• There will be some duplication - due primarily to the INNs not being released with Research Code information, whereas from clinicaltrials.gov they typical enter via a Research Code name - after a few months the entries are linked. So any further information on this set would be greatly appreciated....
• The Phase number refers to the highest phase I could find the antibody drug reaching in the broad literature - it does not capture current status, and in fact a large number of these will have been abandoned by now.
• There are some ambiguities (to me at least) over the USAN year, I use the date the name is published, USAN themselves appear to use a sometimes backdated date, this is probably due to inevitable gaps between assignment of the name and it's publication.

Another paper about ChEMBL

A paper on ChEMBL has just been published in Nucleic Acids Review Database Issue. If NAR is new to you, it is the de facto place for publishing new (and updates to) online biological data sources.

A link to the advance access free, Open Access paper is here.

%T ChEMBL: a large-scale bioactivity database for drug discovery
%A A Gaulton
%A LJ Bellis
%A AP Bento
%A J Chambers
%A M Davies
%A A Hersey
%A Y Light 
%A S McGlinchey
%A D Michalovich
%A B Al-Lazikani 
%A JP Overington
%J Nucleic Acids Research
%D 2011 
%O doi:10.1093/nar/gkr777

A paper about ChEMBL

There is a new paper on ChEMBL just published in Biochem. Soc. Trans. The paper itself is here (subscription required).

%T Collation and data-mining of literature bioactivity data for drug discovery
%A LJ Bellis
%A R Akhtar
%A B Al-Lazikani
%A F Atkinson
%A AP Bento 
%A J Chambers
%A M Davies
%A A Gaulton
%A A Hersey
%A K Ikeda
%A FA Krueger
%A Y Light
%A S McGlinchey
%A R Santos
%A B Stauch
%A JP Overington
%J Biochem. Soc. Trans
%V 39
%P 1365-1370
%D 2011

Gone Fishin'

Things will be fairly quiet for the next week at ChEMBL Manor - we're off on our annual research retreat - this time to Kent. So please allow us a little more time to get back to emails, etc.

Protein Descriptors

Some time ago we asked about protein descriptor services on the web - the long and short of it is that, there really wasn't anything that fit our needs, so we wrote one. Given a sequence it returns a long vector of descriptors, things like hydrophobicity, fraction of each amino acid, pI, and a whole bunch of other stuff. If there is interest, we could open this up as a web service - so return a JSON or XML object in real time (and for UniProt sequences have these precalculated). There will be some licensing issues for some of the descriptors, but I'm sure we can sort something out.

International Chemical Biology Society

There is a new society, that many of the ChEMBL-og readers may be interested in - The International Chemical Biology Society (ICBS). The first meeting is being held October 11-12th 2011 in Kansas City. The program looks great.

Note: As of posting the ICBS website gives me, on my computer, a 'missing plugin' error, but other links seem to work.

Stem Cell Differentiation

Over the summer one of our interns has entered some stem-cell differentiation into a small database - this is based on a literature search, followed by mapping the compounds to ChEMBL entries (or UniProt codes for protein factors). This was an Open Collaboration with Pfizer, who contributed the literature analysis, and also the mappings to the Cell Line Ontology. It is pretty fascinating to be able to control the path of differentiation with things that could potentially, one day, be drugs.

So, we could put this up as a microsite, have the data available for download, etc, if there is any interest?

Integration of a filtered set of PubChem Bioassay data into ChEMBL.

A sub-set of the PubChem Bioassay data has been integrated into ChEMBL.

How is this sub-set defined ?

In PubChem, depositors may assign multiple result types to an assay. However, if an assay is deposited as a ‘confirmatory’ assay (defined as an assay where a range of SID concentrations have been tested, with a view to determining a measurement of potency), then one of the result types must be marked up as an ‘Active Concentration’ (AC) result type. Panel assays may contain many ‘AC’ result types, one per panel member. The AC result type is the calculated potency measurement from the data, and is typically an IC50, EC50, AC50, GI50 or Ki. In addition, the PubChem deposition process requires that each SID in an assay must be assigned a single ‘Activity Summary’, from a controlled vocabulary which includes ‘inactive’, ‘active’ and ‘inconclusive’.

Only assays containing ‘AC’ result types have been integrated into ChEMBL, and from these assays, only activity data and SIDs associated with ‘AC’ result types have been integrated. The ‘Activity Summary’ field in PubChem associated with each integrated activity is also captured and shown in the ‘Activity Comment’ field in ChEMBL. Panel assays are divided into separate assays in ChEMBL, one ChEMBL assay for each panel member.

How are structures normalized ?

An automatic ‘standardization’ of SID structures downloaded from PubChem is carried out prior to integration (using in house protocols). Standard inchis are generated from the standardized mol files, and used to normalize with existing ChEMBL structures. SIDs matching exactly on standard inchi to existing ChEMBL structures are assigned to the existing CHEMBLID (and the mol file already associated with the existing ChEMBL structure is used to represent the searchable structure for this CHEMBLID). Where no match to a standard inchi is achieved, the incoming SID is assigned to a new CHEMBLID, and the standardized mol file for the SID is used to represent the searchable structure. A very small number of SIDs (<0.1%) with standardized mol files that fail to produce valid standard inchis, or to load into a oracle symyx cartridge without errors, are each assigned a new CHEMBLID, and associated with a ‘null’ structure (ie: no mol file is associated with this new CHEMBLID).

How frequently is the integrated data updated ?

Updates are carried out every ChEMBL release cycle.

How are targets mapped ?

Mappings to ChEMBL targets for each integrated PubChem assay has been automated for the initial load. However, manual review of these mappings by expert curators may result in ongoing changes.

How do I filter my query results to exclude or include various data sources ?

Users who prefer to exclude the integrated PubChem data (or any other integrated external data set) from their ChEMBL web-interface searches can do so by clicking ‘Activity Source Filter’ next to the main ChEMBL search bar, and deselecting the sources not required in future searches. Note, however, that these deselections persist between browser sessions. Users querying ChEMBL database dumps directly using SQL, and wishing to achieve this same filtering, should inspect the ‘source’ table, and the foreign keys to this table in the ‘assays’ and ‘compound_records’ tables.

Visiting Speaker - Lipinski 4th October 2011, Wellcome Trust Genome Campus

Chris Lipinski, of Rule of Five renown, is visiting the Genome Campus on Tuesday 4th October 2011 - he will give a talk entitled 'What is the Chemistry in Chemical Biology?'. The talk will be at 4pm. The presentation is open to all, and if you're from off campus, I'll need to arrange access for you (mail me to arrange this).

Please note - it's not possible to broadcast this talk over the web.

Recruitment - Postdoc at the ICR in Computational Biology

From the lab of one of our collaborators comes this job opportunity.

They are seeking a skilled, independent computational biologist with experience of large, multidisciplinary data analysis and programming to develop and apply novel computational techniques to support our cancer drug discovery efforts. They will take the lead in the development and dissemination of the integrative cancer research platform, canSAR.

The position will involve programming, in-silico research in identifying novel cancer therapeutic targets as well as the opportunity to mentor PhD students. The successful applicant will likely have a PhD in computational biology or related discipline, be adept in programming and large scale data analysis. Knowledge in the areas of database architecture, statistics or chemogenomics is advantageous.

Further details, including salary and contract term are available here.