Journal of Cheminformatics and Blue Obelisk

Christoph Steinbeck has posted to the Blue Obelisk List:

I’m delighted to announce that the first open access journal of our
field, the Journal of Cheminformatics, is now live and has published its
first articles. Journal of Cheminformatics is a new open access journal
from Chemistry Central publishing peer-reviewed research in all aspects
of cheminformatics and molecular modelling. It is run by
Editors-in-Chief David J. Wild (Indiana University) and myself (European
Bioinformatics Institute).

Amongst the launch articles are an Editorial by David J. Wild on Grand
challenges for cheminformatics, a Commentary by Steven M. Bachrach on
Chemistry publication – making the revolution and last but not least an
article by Tony Williams and coauthors on Computer Assisted Structure
Elucidation (CASE), one of my own fields of research.

You can view articles and submit your manuscripts at Please share this information with your
colleagues working in the field of chemical information who may be
interested in this new journal.

I have accepted an invitation to be on the editorial board. I take this position with some trepidation as I have grave reservations about the current practice of cheminformatics. It suffers from closed data, closed source and closed standards, and thereby generally poor experimental design, poor metrics and almost always irreproducible results and conclusions which are based on subjective opinions.

I hope to be able to add some weight to improving this situation. The key goal must be that work is novel, useful and reproducible. Too often papers report work done that cannot be transported from inside an institution commited to non-release of code, data or protocols, and often acts primarily as an advert for code, data or people.

The Blue Obelisk is starting to change this. It has consistently argued for Open Data, Open Source and Open Standards (ODOSOS). It’s meeting next week at the ACS – I am very sorry I shan’t be there.

Open Data (and I shall write more later) starting to take off as a concept in chemistry. (It’s much better established in bioscience, astronomy, HEP, etc.). Part of this comes from culture (such as Open NoteBook Science, Chemspider community) and part from better tools for creating or collecting information (e.g. NMRShiftDB, CrystalEye). We also expect that the OREChem project (we meet next week in Redmond) will also have news of Open chemistry data – but I won’t prejudge.

Open Source also continues steadily. Jmol, OpenBabel, CDK, JUMBO are increasingly used as tools in applications. Frameworks such as Bioclipse (and JUMBO-converters) can help integrate these. OSRA looks like being a promising addition for retrieving structures from images and in our own Centre Daniel Lowe has been making very good progress with OPSIN (a name2structure tool which can now be reasnably compared with commercial offerings).

The attraction of Open Source is that it continues to grow and that new helpers come from unexpected places. I will predict that shortly OSRA and OPSIN will start to become integrated in many laboratories and, when they do, even more effort will be added.

Open Standards are also beginning to be seen as important. We were very pleased that Microsoft saw CML and RDF as a future design of chemistry. Open Standards are the most boring, most unrewarding of the three components, but again they continue to grow, however slowly. It is unlikely there will be effective standard bodies in chemistry for some time, so we have to use the power of web toolls such as XML and RDF to help create effective convergence in sematics and ontology. I’ll be blogging more of this later.

I wish J.ChemInf all the best. I know that it took Bioinformatics 5 years to achieve a respectable Impact Factor. I shall publish in J. ChemInf and I urge the referees to be strict – it’s tempting to let through early papers to fill the issues but it mustn’t happen.

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2 Responses to Journal of Cheminformatics and Blue Obelisk

  1. Peter…welcome back to the blogosphere. Thanks for acknowledging the ChemSpider community as a contribution to the Open culture.I know that wasn’t always your view but I hope that our activities have changed your mind. You may be aware of the Open Access ChemSpider JOurnal of Chemistry ( that is now online using our ChemMantis markup system (
    The article that was published in the Journal of Cheminformatics by us regarding Computer Assisted Structure Elucidation will be republished on the ChemSpider Journal of Chemistry with full markup in a similar way as was done here today for a related article:

  2. Pingback: Noticias Edición Digital » Blog Archive » Four short links: 18 Mar 2009

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