Courtesy of Breakfast for Dinner

I was recently alerted by someone about chunks of text copied from an editorial by my colleague David Wild in the Journal of Cheminformatics [1] appearing in another article by Nutan Prakash and Dinta A. Gareja in the Journal of Proteomics and Bioinformatics [2]. While David’s article is cited as a reference, those larger chunks of text are clearly not identified as being his words.

A closer investigation reveals that large chunks of text [2] are copied from other sources. The introduction is copied from the Wikipedia article on Cheminformatics as well as from an article by  Aktar and Murmu and one by Karthikeyan and Krishnan. The latter is cited but the first two sources are not. Generally, citations for these questionable cases appear only as references at the end of the text and are not marked in the text.

It is a common misconception that text from wikipedia can be freely abused. The license says:

Re-use of text:

• Attribution: To re-distribute a text page in any form, provide credit to the authors either by including a) a hyperlink (where possible) or URL to the page or pages you are re-using, b) a hyperlink (where possible) or URL to an alternative, stable online copy which is freely accessible, which conforms with the license, and which provides credit to the authors in a manner equivalent to the credit given on this website, or c) a list of all authors.

Although David’s original article is cited and therefore I think formally the original license was not violated, this somehow feels a little disturbing and I would appreciate your comments on this.

In my opinion, this text [2] is clearly a patch-work of unaltered text from other sources without original contributions from the authors and should not have been published.

References:

[1] David J Wild, Grand challenges for cheminformatics, Journal of Cheminformatics 2009, 1:1

[2] Prakash N, Gareja DA (2010) Cheminformatics. J Proteomics Bioinform 3: 249-252.

In Goslar's old town ((c) Philipp Andre)

There are a few seats left for the 5th German Conference on Cheminformatics in Goslar and we’ll extend the deadline a bit to give you the chance to register if you haven’t done so.

The GCC is a great chance to meet with around 200 other participants from all areas of life science informatics and listen to talks about the latest research in the field. This year we have an exciting collection of keynote speakers with topics ranging from modelling of biological systems and systems chemistry via computer-aided material design to the latest developments in ChemSpider.

The program is complemented by 60 posters and again prices will be awarded for the three best posters.

Goslar itself is a wonderful place to visit, with its two UNESCO world heritage sites, the old town centre and the ore mine.

We are looking forward to meeting you in Goslar. Registration is still open.

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.

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.

Image courtesy of emhuwar

The Cheminformatics and Metabolism group at the European Bioinformatics Institute (EBI) in Hinxton, Cambridge, Uk, has an opening for a phd position. The EBI is one of four outstations of the European Molecular Biology Laboratory (EMBL) and is a great place to do research in chemistry, cheminformatics and drug discovery. In all of these areas, the really exciting stuff is done at the boundaries of molecular biology, chemistry, nanoscience, etc, and EMBL is the place for such interdisciplinary research. The really cool thing and a well-hidden secret: The successful candidate will be enrolled at the University of Cambridge and eventually get a phd from UCam. Back to the records:
The Steinbeck group does research in metabolism, natural products and cheminformatics algorithm development. The successful candidate is free to choose from a range of topics (see below) or suggest his or her own project.
Applications need to be submitted by 15 July 2009 through the EMBL phd programme and ideally the candidate should clearly indicate that he/she has a preference to work with us here at the EBI.

Here are a two suggestions for potential projects

a) Structure elucidation of unknown metabolites based on mass spectrometry or proton NMR. This topic is of great importance for Metabolomics and metabolism research in general, both of which are current hot topics in molecular biology. We have a long standing history of research in this area (see our publication list) and the candidate will be able to build on existing knowledge.

b) Intelligent systems for extracting information from the chemical literature
A vast amount of knowledge is hidden in more than 100 years of chemical literature – knowledge which needs to be semantically annotated and made discoverable and interpretable by computational algorithms. Now, a scientific article in chemistry is a complex mixture of different information and data types. It contains plain text, analytical numerical data in various flavours as well as graphics of all kinds. Methods have been developed to extract of re-discover information from either of these areas. The project here aims at combining information extracted from text, tables and graphics and using each of the areas to validate data from any of the other areas.

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.

Downtown Salt Lake City, Image courtesy of A4GPA

I’ve just arrived at the ACS meeting in Salt Lake City. The trip was a real nuisance, 19 hours or so, and I always ask myself why I do this stuff.Still, after a fantastic breakfast in my even more fantastic hotel, the Grand America Hotel (review pending), and now being at the meeting, is is again great to meet all the usual faces and see some great talks. For cheminformatics and chemical information, there is really no other meeting in the world with such broad attendance from the community.

My first impression from the meeting is that it is probably a little less well attended as the previous ones I’ve been to and that also the number of exhibitors has dropped significantly. This maybe partly because of the problematic economic situation but there have also been emails of companies expressing discontent with how the ACS has treated them in the past.

My program: I will

• give two talks, one about open source for chemistry teaching in one of the CHED sessions on Monday morning, and another one in CINF general papers on Thursday morning on Machine Learning methods for proton prediction.
• participate in the CSA Trust Board meeting on Sunday,
• participate in the InChI subcommittee meeting on Monday
• participate in the CIC-CINF working group meeting on Wednesday
• co-organize the Blue Obelisk Dinner on Wednesday evening.
• go to each and every CINF reception and Harry’s party

It looks like there is not much time for anything else but there are number of interesting sessions and individual talks here. The meeting is emphasizing chemistry’s role in nanotechnology, which of course is a very timely and exciting topic.