SteinBlog » Open Data

Do a cheminformatics PhD thesis at a world-class institution

Christoph Steinbeck — Tue, 16 Jun 2009 13:02:18 +0000

The European Bioinformatics Institute (EBI)

If the pompous title caught your attention, and you are ashamed of that: Don’t worry. It is all true. My cheminformatics and metabolism group at the European Bioinformatics Institute (EBI) is looking for a phd student this year and all you need to do is apply through the regular route. The range of possible topics is wide open, going from metabolomics via automated structure elucidation of metabolites to mining chemical information from the printed literature, and more. Your own suggestions are of course welcome.

The EBI is the world’s largest open provider of biological and chemical information.We are located, together with the Sanger Institute for Genome Research, on the beautiful campus of Hinxton Hall, a few miles south of Cambridge.

One of the small lakes on the Wellcome Trust Campus in Hinxton

Our PhD students are enrolled with the University of Cambridge.

The important part for now: The application deadline for the Fall PhD selection is July 15, 2009. And: Please drop me a note if you applied.

ChEBI release 57, now with links to NMRShiftDB

Christoph Steinbeck — Wed, 27 May 2009 12:29:09 +0000

Congratulations to the ChEBI team for publishing ChEBI version 57.

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/

ChEBI chemistry ontology development funded by BBSRC

Christoph Steinbeck — Tue, 19 May 2009 11:30:45 +0000

We received our official award letter from BBSRC Tools and Resources Fund today for the ChEBI ontology development grant. Needless to say, we are thrilled. We are now going to work together with Michael Ashburner’s group at the University of Cambridge to align ChEBI with other OBO Foundry ontologies by adoption of the Basic Formal Ontology and the Relationship Types Ontology.
This will include extensive annotation of the ChEBI ontology required after adoption of BFO and RO. The adoption of the BFO will require a major reorganisation of the upper levels of the ChEBI ontology in order to allow it to align to the BFO. This
reorganisation can only be achieved by manual annotation although some semi-automatic means will be employed to aidthe curator. In addition to the reorganisation of the upper levels, new relationships will be introduced semi-automatically but as the ChEBI ethos requires that all data is manually checked to maintain ChEBI’s high standards of data quality, we expect a major annotation task. The project is funded for three years. Stay tuned. We’ll report on our progress on a regular basis.

NMRShiftDB now with more than 12.000 proton spectra

Christoph Steinbeck — Thu, 14 May 2009 17:10:51 +0000

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.

ChEBI behind the scenes

Christoph Steinbeck — Fri, 08 May 2009 08:12:37 +0000

With ChEBI release 56 behind us, I thought I’d share some insight into how ChEBI is created and what we do to prepare a release. In the last years, the ChEBI team on average consisted of two software engineers maintaining and improving the software and two to three curators doing the data entry and curation. It is remarkable, that, by now, the question of which chemical compounds make it into ChEBI is completely community driven. Requests to enter compounds are submitted by users and other database maintainers via the ChEBI curator request tracker on SourceForge. Besides increasing the public knowledge of mankind, the biggest benefit and driving force for submitters is the assignement of a stable ChEBI identifier which then can be cited and linked to from other resources.

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.

3rd International Biocuration Conference in Berlin

Christoph Steinbeck — Fri, 17 Apr 2009 07:24:52 +0000

Berlin Dahlem-Dorf tube station

I’m attending the 3rd International Biocuration Conference in Berlin, which looks like a pretty successful meeting in terms of numbers of participants. Seems like somewhere between 100 and 200 participants. It looks like the time for recognition for biocuration and curated biological resource has come. The International Society for Biocuration has been inaugurated yesterday. People from publishing companies such as Nature are attending.

Janet Thornton, director of EBI, gave the opening keynote yesterday evening, rehearsing some of the history of biocuration and looking into the future of securing funding for biocuration through the Elixir project.

I’m now listening to Philip Bourne talking about “Changes in Scholarly Communication and the Potential Impact on Biocuration”. He talks, beyond a lot of other things, about the author embedding semantic information into the orginal manuscript and introduces part of his own work with Microsoft on a plug-in for word to do this enrichment.

There is nothing overly particular about this meeting but it strenghens my feeling that we are at the point where finally the idea of preserving the information in the first place, in the scientific document, has come. Both Dietrich’s semantic enrichment conference as well as this one was well attended by publishers – Elsevier and Nature where at both. This scientific document can then become both a scientific article as well as one or many database entries.

Another notion that has come up a couple of times is the question of reward for authors to make and submit semantically rich documents. One of the ideas is fast-tracking those documents – publishing them faster.

ChEBI at the Fall 2009 ACS meeting in Washington

Christoph Steinbeck — Fri, 27 Mar 2009 15:05:23 +0000

I’ve been invited to present our ChEBI ontology at the 2009 Fall Meeting of the American Chemical Society. Here is our abstract:

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.

“new open source era … for better drugs”

Christoph Steinbeck — Tue, 03 Mar 2009 13:32:15 +0000

As we learn from a rather poorly written article over at xconomy, “Biology has never really had a social-networking movement like open-source computing, where thousands of loosely-affiliated people around the world pool brainpower to make better software”. If you translate that into what was needed for biology (or chemistry) according to the xconomy author, it would translate into a “social-networking movement where thousands of loosely affiliated people around the world pool brainpower to make better biology”. Now, I leave it to you extremely bright guys out there to figure out why I think that already exists and how it is called.

At least, the article informs us about lots of money being pumped into another collaborative effort to exploit systems biology to make better drugs, which might be a good thing. I’m having a hard time to understand the fundamental difference between this and existing open approaches, but I’m happy to learn. Part of this lack of understanding comes from a lack of meat in this article. Maybe one of my readers can comment.

Industry-funded medical research will double your impact factor

Christoph Steinbeck — Mon, 16 Feb 2009 09:00:52 +0000

The Guardian has a nice piece by Ben Goldarcre reporting about a study published by the British Medial Journal entitled “Relation of study quality, concordance, take home message, funding, and impact in studies of influenza vaccines: systematic review”. Both the newpaper article and the study are worth reading and seem to be open. Besides many other interesting findings, the BMJ article finds that the journal impact factor of industry-funded studies of influenza vaccines (both Ben and I find it quite likely that this is not limited to the study of influenza vaccines ) are on average more than twice as high as those for purely academic studies (Impact Factor 3.74 vs 8.78). Judge yourself.

4th German Conference on Chemoinformatics

Christoph Steinbeck — Sat, 12 Jul 2008 12:05:14 +0000

The Chemistry-Information-Computer (CIC) division of the German Chemical Society announces the 4th German Conference on Chemoinformatics (22. CIC-Workshop) to be held in Goslar, Germany, November 09-11, 2008.

This international symposium will address a broad range of modern research topics in the field of Computers and Chemistry. Focus will be on recent developments and trends in the fields of Chemoinformatics and Drug Development, Chemical Information, Molecular Modeling, Computational Material Science and Nanotechnology and other highlights in the field of Computational Chemistry. The scientific program will include plenary lectures, short lectures as well as poster presentations. Furthermore, there will be a pre-conference workshop on Sunday.

I would like to highlight this year’s session on Open Access Publishing in Chemistry where we are going to investigate what’s happened and changed since our last session on this topic a few years ago.

Conference Web site:
http://www.gdch.de/gcc2008

Conference Venue: Hotel Der Achtermann, Rosentorstrasse 20, D-38640 Goslar, Germany.

If you register, you might want to take into account the conference dinner on Tuesday evening, which is included in the conference fee and typically a very nice event. Therefore, you should prepare to leave on Wednesday morning.

Goslar is located at the heart of Germany and famous for its ore mine (UNESCO World Heritage Site) and its old town.

Invited Speakers:

Jürgen Bajorath
Michael Berthold
Marcus Elstner
Robert Glen
Kurt Varmuza
Brian Andrew Vickery

Dead Lines:

Submission of oral contribution: 29.07.2008
Submission of posters: 29.07.2008
Scholarship: 29.07.2008
Submission of last-minute-poster: 28.10.2008