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 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.

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/

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.

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

Peter Murray-Rust set the scene by emphasising the importance for Open Data. He showed some fantastic work on data extraction by OSCAR from theses, where his group had parsed a synthetic chemistry thesis into an interactive graph of a reaction network. He also showed an SVG animation of this graph as a reaction sequence, all automatically generated from an OSCAR run. Peter pointed out in the subsequent discussion that data cannot be copyrighted, which was acknowledged by all publishers in the audience. The reality is different, however, because publisher’s licenses often prevent downloading of more than few articles in a row. Detection of a robotic download for text mining comes with the danger of the whole university being disconnected. It is unclear to me how robotically parsing papers and extracting data would damage the bushiness model of publishers. It could, of course, lower the number of subscriptions from

Ian RusselL of ALPSP presented on Open Access models and how those of uses by ALPSP members. He pointed out that a lot of long-tail publishers publish only two or three journals, quite in contrast to ACS and RSC, for example. He stated that making profit is good, because it can be reinvested into innovation. I’m not sure if I’ve seen much innovation in the publishing business before the emergence of the Open Access model. He further commented on self-archiving stating that only pre-peer-review manuscripts can be self-archived without permission from the publisher. A librarian in the audience pointed out that duplication of costs by mixed read-pays and author-pays models have significantly increased the libraries expenses and Ian Russell comment was that there are no cost-savings in Open Access. Not sure if this helps. My impression is that it is not in the interest of publishers to resolve this conflict. [Editorial Note after Submission: Ian has replied to this part - See comments. ]

Robert Kiley, Wellcome Trust, summarized the Trust’s OA policy, where Trust-funded research needs to be put into pubmedcentral six month after publication. If I remember right, the Trust funds more than 90% of Biomedical research in Britain. The NIH now has a similar policy, and so has European Research Council; Robert mentioned that most text mining so far is based on PubMed abstracts, but that the full text would be required for serious efforts. He further pointed out that the number-one option for researchers to comply with the Trust’s OA policy would be to publish in a true Open Access Journal (BMC, PLOS, etc.). The second-best choice would be to publish anywhere and self-archive. The least preferable choice would be to publish with the ACS (one of the very few publishers without a Wellcome-Trust complient OA policy) and try to change the copyright notice . The Trust is in contact with publishers to make sure that authors have a wide variety of journal with open access policies to choose from. Robert highlighted the importance of OA for the long-term preservation of articles and data therein, with special emphasis on future-proofing the record of medicine. To check the compliance of authors with this new OA policy, the Trust conducted a study with 279 papers on Trust-funded research, where, if I remember right, over 90 percent of researchers were in compliance. Robert concluded his talks with mentioning UK PubMedCentral, which will be exposed for Text Mining, including Chemical Entities. The trusts next steps are to continue to work with publishers, monitor compliance of researchers, make funds available for OA and develop UkPMC

My own talk went about Chemistry at EBI and in European Bioinformatics in general.

Simon Coles, University of Southampton, talked about building repositories to preserve chemical data and publications. His view is that of an active crystallographer and he pointed out that this community could serve as a paradigm for other areas of chemistry. He pointed out that spectra are often published as inaccessible supplemental information without proper guidelines for representation. A great chance for capturing and publishing data in the very beginning are movements like OpenWetWare and Open Notebook Science which are catching and publishing laboratory experiments as they are done, and not 9 month after, when published and filtered. Simon mentioned that less than a quarter of cystral structures determined are actually published – a lot of data is just lost. This is certainly true for NMR data, an area of interest of my own research. The crystallographic community has made a step to increase the number of published crystal structures by creating Acta Cryst E (now open access) where publications just consist of the crystal structure it self and a few additional remarks. They just publish the crystal structure!!! In CIF format, computer-readable and harvestable. This would be a great step for NMR – publish structure and spectral evidence, semantically enriched, in a short communication. Simon further reported that Southampton has build the eCrystals Data Repository software based on the eGrid project, where crystallographic data can be easily deposited, supported by authoring tools, and serving as a laboratory archive. An embargo mechanism is implemented but once published, data can be harvested and analysed. The whole, funded study was really about preservation of research data, exemplified on Crystallographic data. To scale this up, Simon suggested (does is exist already?) to have a Federation of Crystallographic Data Repositories. He further mused about how that could be transferred to less well organized disciplines such as NMR, synthesis, etc. Long tail science is extremely fractioned, unorganised stuff sitting on Laptops, unorganised, inaccessible. A new kind of electronic lab notebook, the “Smart Tea Project“, can actually be taken into the lab, using mobile input devices. Analysis and discussion of on-the-fly captured data can then be published in the workgroup, between collaborators in the world, using blog-technology. Some software can enable machines and sensors to blog their results – a sensor for room temperature and or air flow in the lab for example can then be correlated with outcome of NMR experiments using time stamps.

Diana Leitch, University of Manchester, gave “the academic librarian’s perspective, in a unique way of just talking and *not* showing any slides How relieving.

I had to miss the two talks by Chris Leonhard from BMC, whose title seems to indicate growing support for Open Access and by by David Hool from the Nature Publishing Group, because I had to catch my flight from Stansted, which I also almost missed because the fantastically reliable British rail system – all trains from London to Stansted were cancelled, we were advised to take a local train to a small station in the middle of nowhere instead, where of course there was nothing like a connection to Stansted. I was one of the lucky few to get the last available taxi, driven in snail speed by an old lady Could have been very funny as a movie. Well, I made it to the gate in time, where “the machine was otherwise fully boarded and awaiting and an on-time departure” (Those of you travelling with Ryan Air regularly know what I’m referring to). I will never again be arrogant toward people showing up in Stansted sweating and on the very last minute. The all come from central London.

So, what it the bottom line from this meeting? The important message is perhaps that OA publishing has not yet quite reached chemistry but that there are grass-root movements which are going to revolutionize the way in which we publish science and scientific data, starting at the very first moment when research is performed in the lab.

CBCNews has an article.

The article mentions about 2500 substances to be listed in the database. An interesting feature of this Human Metabolome Database is an NMR and MS spectrum search. Unfortunately, the search does not feature an overly flexible similarity function but after some tweaking of parameter, one can get a result. A list of carbon NMR shifts such as “10, 20, 30, 110, 120, 200″ yields results if you increase the shift tolerance to 5ppm and lower the similarity threshold to 50. Note that all of the NMR spectra you get in this result list are predicted and not measured.

Our group here at Cologne University Bioinformatics Center (CUBIC) maintains an NMRShiftDB, which could be used as a source for measured NMR spectra in this project.