Courtesy of Andres Rueda, Flickr

There are still places available at the 2012 conference on Therapeutic Applications of Computational Biology and Chemistry (TACBAC), 12-14 March 2012, at the Wellcome Trust Conference Centre, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK

This conference will bring together leading researchers investigating computational chemistry and biology techniques as applied to advancing our ability to predict, diagnose and modulate human disease. This broad and multidisciplinary meeting will explore the major challenges in drug discovery and development where innovation in computational approaches and tools can really make a significant and tangible contribution towards novel treatments.  You should attend this conference if you are a researcher interested in drug discovery, or developing or using computational approaches to the development of therapeutics, or if you are a key decision maker in a pharmaceutical or biotechnology company.

Each of the sessions, which progress from identifying disease mechanisms to implementing new therapeutic and diagnostic approaches in the clinic, will bring together experts in both the biomedical and the computational aspects of the topic under discussion. Sessions chairs will encourage discussion and contribution from the attendees.

Session topics
• Clinical implications of individual genomes
• Metabolism and biomarkers
• Computational systems biology
• Discovery of chemical probes
• Modelling xenobiotic metabolism

Registration and submission of abstracts is open now.

ChEBI Release 57 now contains links to NMRShiftDB. Search ChEBI for “caffeine”, for example, and you find the link to the carbon NMR spectrum of caffeine on the “automatic XREFs” page of ChEBI, in the “Small Molecules” section.

ChEBI now contains just under 17,963 manually annotated entries of which 108 entries have been submitted via the ChEBI Submission tool  (www.ebi.ac.uk/chebi/submissions). The next ChEBI Release will be on the 24 June 2009.

See our entity of the month, Oseltamivir.

All data are also available on the public FTP site:
ftp://ftp.ebi.ac.uk/pub/databases/chebi/

Assigned proton spectrum in NMRShiftDB

The number of structures and spectra in NMRShiftDB now exceeds 31.000 and 35.000, respectively. The number of proton spectra alone is now 12.934. This is due to NMRShiftDB developer Stefan Kuhn in my group importing a recent donation from our collaborators Reinhard Dunkel and Heinz Kolshorn. Thanks to Heinz and Reinhard for their generosity.

With ChEBI release 55 we have introduced the new submission tool which now allows our submitter to create ChEBI datasets themselves which a) gives our users more control over what they want to see in ChEBI and b) saves our curators some duplicate work.

In preparation for a release, here is what the ChEBI team does.

• Create automatic cross-references to PubChem, UniProt, IntEnz, BRENDA, SABIO-RK, ArrayExpress, IntAct, Patents etc…These are all run a week before the release and are based on ChEBI identifier matching or text matching.
• Annotation of entity of the month
• Submissions deposited directly into the database by users are processed by our annotators.

On the release day:

• Data is exported overnight into multiple formats, OBO format, SDF, Oracle data dumps and PostgreSQL/MySQL dumps.
• Public web site updated with the entity of the month.
• Statistics generated and stored.
• Sitemaps are generated to be used by search engines like Google for indexing.
• Finally data is deposited into PubChem and the EB-eye search engine is updated.

We are pleased to announce release 56 of our database of Chemical Entities of Biological Interest (ChEBI).

SDF files are now available with ChEBI Release 56. They can be exported via the Downloads section or the search results page. We also have automatically generated links from IntEnz (www.ebi.ac.uk/intenz) and Rhea (www.ebi.ac.uk/rhea). This release contains 17842 annotated chemical entities (and not compounds, as I wrote earlier – we also have classes of compounds and abstract concepts) with 74 of them new submissions entered via the ChEBI submission tool. The next ChEBI Release will be on the 27 May 2009.

See our entity of the month, Ethyl formate.

All data are also available on the public FTP site:

ftp://ftp.ebi.ac.uk/pub/databases/chebi/

The workshop itself was phantastic – we had 40 participants with well balanced contributions from industry and academia. The first half day was dedicated to tutorials on various aspects of CDK, basic installation, our CDK and Oracle-based chemical search engine, scripting of CDK from within Bioclipse and CDK-based workflows in KNIME. The second day brought talks about science and applications based on CDK by John van Drie, Asad Rahman und Oliver Karch.  I reported earlier on those talks.

This official part was followed by a developers workshop in the format of an unconference.  Participants suggested topics on the fly and then voted with their feet. The topics that then made it where:

• Clojure
• Mining ChEMBL with CDK pharmacophore stuff
• Threading group
• Top 10 improvements (CDK WS 2009 unconference)
• JChemPaint/Rendering

all of which reported their results on the CDK wiki.

Another important outcome was a movement to join forces in creating and maintaining joint CDK-based plugins for KNIME and Bioclipse. There is a lot of synergy to be harvested. Licensing problems will need to be overcome but that seems doable.

As anyone can read on our CDK homepage, the CDK was started because my old compchem java classes that I had written for the first version of my structure elucidator SENECA and which where also the basis for the first JChemPaint releases needed a re-write (they where actually not bad and pretty fast, but not really object-oriented). By that time, friend Egon had come on board and so we took advantage of a joint visit to Jmol creator Dan Gezelter at Universtiy of Notre Dame to start the redesign. Unfortunately, we lost the two screenshots from Dan Gezelter’s whiteboard at nd.edu where we sketched the object hierarchy which is still largely in place today.

So, here is the current status of CDK in numbers:

• In September 2009, CDK will turn 9 years old and we already start planning for the 10th anniversary workshop.
• Its code base is more than 90,000 lines of code in more than 900 classes and over 9000 methods.
• As of today, 20/04/2009, CDK on Sourceforge has 67 registered developers and
• 86 (111) people are subscribed to the cdk-devel (cdk-users) mailing lists.
• According to Ohloh, CDK is now worth $ 4.6M and took an effort of 84 person years to create.
• The CDK article published in 2003 has been cited 68 times according to Google Scholar (I could not get my VPN to work so I do not know what WebOfScience says about our current citation count)
• According to SourceForge, CDK has been downloaded 90,000 times since 2001.

On the first workshop day, we’ll have tutorials on

• How to get started with CDK, given by Egon Willighagen
• CDK and databases, by Mark Rijnbeek
• CDK and Bioclipse, by Ola Spjuth
• CDK Workflows in KNIME, by Thorsten Meinl and Bernd Wiswedel

followed by the workshop dinner and a second day with scientific talks John van Drie, Asad Rahman and Oliver Karch.

The final discussion will include a presentation by Mark Forster, Syngenta, on his observations on the usability issues of CDK in industry. We also owe Mark a lot for creating the freely distributable linux image with the CDK and all the CDK related software used at the workshop.

On Tuesday afternoon we’ll have a developers workshop, which, traditionally, has the format of an unconference. The ideas for this format are taken from a concept called “Open Space Technology“, which we only discovered after having practised them for more than 5 years . To be fair, OST conceptualizes things nicely and relieves one from figuring out how to run meetings as openly as possible. Citing from the Wikipedia articles linked above, the idea is to have a facilitated, participant-driven conference centered around a theme or purpose, in a self-organising process; participants construct the agenda and schedule during the meeting itself.

A facilitator (me in this case) introduces the principles of OST to the participants. Participants then write the title of a session they would be interested in on a piece of paper, walk to the front of the auditorium and announce the title. If a participant proposes a topic, he or she should be passionate enough about the topic to lead the respective session.

OST philosophy is based on four rules and a law:

1. Whoever comes is the right people: this alerts the participants that attendees of a session class as “right” simply because they care to attend
2. Whatever happens is the only thing that could have: this tells the attendees to pay attention to events of the moment, instead of worrying about what could possibly happen
3. Whenever it starts is the right time: clarifies the lack of any given schedule or structure and emphasises creativity and innovation
4. When it’s over, it’s over: encourages the participants not to waste time, but to move on to something else when the fruitful discussion ends

There also exists another tentative “law”, usually referred to as the “Law of Two Feet“ (or “The Law of Mobility”), which reads as follows: If at any time during our time together you find yourself in any situation where you are neither learning nor contributing, use your two feet. Go to some other place where you may learn and contribute.

Having said all this, I hope that this largest CDK workshop ever will be asuccess and most importantly fun for everyone. We’ll keep you informed at the CDK 2009 Workshop wiki page.

ChEBI – An open ontology for Chemical Entities of Biological Interest

Paula de Matos (1), Kirill Degtyarenko (2), Marcus Ennis (1), Janna
Hastings (1), Inma Spiteri (1) and Christoph Steinbeck (1)

(1) European Bioinformatics Institute, Hinxton, Cambridge, UK
(2) European Patent Office, The Hague, The Netherlands

Chemical Entities of Biological Interest (ChEBI) is a freely available, manually annotated resource providing data such as chemical nomenclature, an ontology and chemical structures. The ChEBI ontology imposes meaning onto the data according to four subontologies: molecular structure, application, biological role and subatomic particle. As a cheminformatics resource it provides chemical substructure and similarity searching using the Chemistry Development Kit (CDK). ChEBI annotates structures with various properties such as charge and mass and names including brand names and International Nonproprietary Name (INN). This extended coverage is complemented by manually annotated names appearing in Patents and Patent identifiers. In addition names can now appear in French, German, Latin and Spanish. Acting as a chemoinformatics portal to other bioinformatics resources, ChEBI has introduced automatically generated links to resources such as UniProtKB, IntAct, ArrayExpress, SABIO-RK or PubChem. ChEBI lives at http://www.ebi.ac.uk/chebi/, where it is also available for download in
a variety of formats and accessible via webservices.