Revised Glycan Nomenclature System

C&EN has highlighted the recent revision of the CFG (or “Essentials”) nomenclature for the structure of complex glycans. The revised nomenclature is posted on the NCBI site, which will be part of the upcoming third edition of Essentials of Glycobiology. The new nomenclature now includes a longer list of monosaccharides, which will be a welcome addition for anyone working on non-vertebrate glycans (especially bacteria or plants). There are also some changes to the use of color, with white symbols being reserved for unassigned monosaccharide stereochemistry (often the case with structures confirmed only by mass spectrometry). Colors are then reserved for specific stereochemistries of monosacharides, so a generic hexose is a white circle and Glc and Gal are blue and yellow, respectively. Many of these colors overlap with previous use in earlier nomenclature, so those that know the system for mammalian glycans should be able to read the revised system without much trouble.

If you need to draw your own glycans, the CFG site has a free tool for this: Glycoworkbench. Note that it still appears to use the 2nd edition nomenclature. The current link for that doesn’t seem to have an obvious link to the software, but you can find a version here.

RSC takes Chemical Science open access

To follow up on the last post regarding open access journals in the chemistry space, it looks like Chemical Science will be going to a gold open access model. The most notable feature here is that the publisher says they will waive any publication charges “for at least two years.”

This seems like a serious move from RSC, and one hopes that other chemistry publishers will follow suite.

For comparison to other gold open access chemistry journals, some stats on Chemical Science (in 2013):

  • Chemical Science, $0 (until at least 2016), 596 articles (658 if you count front/back/cover material)

Open access publishing in Bio/Chemistry – Whatever happened to PLoS Chemistry?

I’ve been a fan of the open access (OA) movement for a while. However, I can’t say that I’ve voted with my feet: I typically publish in society/specialty journals that are not open access. Of course, some of these publishers now give you the option of paying them to make your paper OA, so they can argue that one can still publish in those venues and just pay to allow access to your work.

I’m not a fan of this model – having an essentially random sampling of papers does not make for a good presentation to the reader, nor does it address the idea that an open archive of research data and conclusions is a benefit to the community. I would argue that opting to pay OA charges at these closed journals is basically supplementing the journal’s advertising budget with your research grant. At the end of the day, if readers want full access they must get their libraries to pay for the rapidly growing cost of closed journal subscriptions.

Which brings me to the subject of this post: What are the best OA venues for chemists to publish their work right now? I’m specifically interested in “gold road” journals, those that make their content freely available immediately upon publication. Here’s the list I put together in an hour or two of searches, I was targeting Organic Chemistry, Chemical Biology, Biochemistry, and related fields. I doubt this is exhaustive, and I’d appreciate any suggestions from others. (Journals listed with current publication charge, and number of articles published in 2013):

Clearly PLoS One is the largest venue, Scientific reports seems to be growing (about a 3X increase from 2012-2013). I hadn’t realized until now that Molecules, Arkivoc, and the Bielstein journals were OA. Some of the ones low in the list may need some incubation time to reach critical mass. I ruled out some smaller journals if they were not indexed on Web of Science, PubMed, or SCOPUS. Any others that I’m missing?

There was once some talk of a PLoS Chemistry, but I can’t seem to find any indications that its happening. I don’t see many of these venues competing with premier society level journals without buy-in from leaders in the field. My impression is that this has allowed the PLoS brand to take off, with a few of those journals having become top-tier venues.

Its worth noting that archive servers are a mechanism for OA publishing. This is dominant in some field (but sadly lacking in Chemistry/Bio):

bioRxiv.org is the new kid on the block here, and it remains to be seen how readily preprint servers are become adopted in biomedical research.