; void 0;){kind=small}
Feedback from C and E News
Posted by: Antony Williams in UncategorizedCopyright©2009 Antony Williams
Steve Ritter from C&E News has given some wonderful feedback to my previous blogpost regarding where does C&E News source its structures. I admit to being overjoyed to have someone from the ACS organization respond in such a willing and open way regarding their processes as my previous attempts to connect with the organization regarding Open Data were interesting in a very different way (1,2,3). I will be following up with Steve to say thanks and see how we can help source structure images for him if necessary. I’ve copied his comments below and have inserted my own into his post.
Steve Ritter said:
Thanks to Antony for pointing out the mistake in the C&EN structure. I did inadvertently leave out the stereochemistry at the methyl on the side chain, and the geometry for one of the double bonds is incorrect.We publish several hundred structures per year in our 51 print issues and on our website, and inevitably we get some wrong–on the average five or fewer per year that I am aware of.
AJW> Steve and his colleagues do have a tough challenge as their efforts are seen by thousands of people every week and with the variation in quality out there it is not difficult to generate some mistakes. My experience would support his estimates.
We are grateful to our readers for pointing out the mistakes. In this case, a revised structure is being posted on our website and a correction will run in an upcoming print edition. Please check to see that the new structure is correct.
AJW> The one on Wikipedia has been edited by me tonight. Steve…feel free to grab the image from Wikimedia Commons here.
As for where we source our structures, our primary source is the researcher and peer-reviewed papers, because many compounds are novel. For known compounds, knowing that those can sometimes be wrong in papers, we always double check them against one or more primary sources, typically Merck Index and SciFinder.
AJW> I gave three ladies from the Merck Index at the ACS in Salt Lake City an overview of ChemSpider and they GAVE ME a copy of the latest Merck Index. I agree..it’s a RICH resource of correct and valid information.
Although CAS and C&EN are both part of the ACS Publications Division, we at C&EN still have to pay for our SciFinder access, strangely enough.
AJW> It’s not a surprise that they have to pay as I have experience of Fortune 500 America and “internal services” cost. But, it’s a shame that cost might have been barrier here, if it was.
To tell a woeful story, one that demonstrates it is never easy to make sure a structure is “correct,” I received a structure of domoic acid from the researcher I wrote about, as there was not one in the paper. But the structure was wrong–it was missing a methylene in one of the short carboxylic acid side chains. The researcher was not aware of that until I pointed it out, and that structure had been used in several published papers already. I noticed the error by checking the structure in the Merck Index.
When it came time for our artist to draw the structure, I did not really like its orientation in the versions I had. I checked SciFinder, and the structure there is identical to the Merck version, but SciFinder does indicate the absolute stereochemistry. I also checked the Web, and found the Wikipedia entry and several other references with the structure. As Antony noted, domoic acid is well known in the literature, but one sees it drawn myriad ways. I liked the orientation of the Wikipedia entry the best, and used that as a model to draw out the structure by hand for our artist to redraw. I checked my version against Merck, but I was focusing on the double bond geometry and missed the stereocenter when I drew it. That’s the long-winded version.
AJW> Steve, I am smiling at your long-winded version. Been there, done that. It’s HARD work!
It’s embarassing to make any kind of mistake, especially in C&EN. But it is a bit more so for me because every structure that appears in C&EN comes across my desk for scrutiny. It’s not the first time I missed something in a structure, and probably isn’t the last. We have a great staff of writers and editors that make such mistakes rare.
AJW> Join the club. It’s easy to make mistakes with complex structures. That’s why a public resource of validated structures is critical and I believe a combination of Wikipedia, Wikimedia Commons and ChemSpider can provide exactly that, with time.
As a rule, we at C&EN don’t use Wikipedia as a primary source for structures or chemical information, and I recommend that policy to anyone. We don’t even use articles or structures previously published in C&EN as a primary source without rechecking, in case we made a mistake the first time around. The only two sources for checking structures that I really trust are Merck Index and SciFinder, with Merck being a little better because sometimes the SciFinder structures are drawn awkwardly, but that is just my personal opinion.
AJW> I agree with your opinion regarding structure images in SciFinder. They are far from attractive BUT they do carry clear nomenclature on the image which is VERY necessary for structures such as ajmaline.
It would be nice to have an authoritative web-based source of standard, well-drawn structures for chemists to go to so they can freely cut and paste structures into their papers, PowerPoint presentations, and anything else they might need. Maybe Wikipedia will be that source one day.
AJW> For encyclopedic articles I agree..and we are working on it with the team with our Wikipedia services. We discussed today on the Wikipedia Chemistry IRC Chat the need to change the display format for structures to ACS settings and will do so. For the other millions of structures that don’t make their way to Wikipedia then ChemSpider can provide that role.
As for the structure of domoic acid on the NOAA page that Antony noted, I believe the stereochemistry for each of the three ring carbons is backward.
AJW> High five!
Apologies for rambling on, but thanks again for pointing out our mistake. We at C&EN know we are considered authoritative and held to a high standard by the chemistry community that we serve, and accuracy is paramount to maintaining that trust. We take our responsibility seriously.
AJW> Steve..I am happy you took the time out of your day to post here. It shows a true commitment to your responsibility and intentions to provide high standards of support for us all. C&E news is a weekly read for me and I respect your work. My thanks to all of your colleagues for a great magazine.
![Reblog this post [with Zemanta]](http://img.zemanta.com/reblog_e.png?x-id=6889b692-9c17-41a1-859b-c8df126284a9)
Stumble it!
Entries (RSS)
April 17th, 2009 at 9:08 am
Indeed, a very helpful response. I interested in Dr Ritter’s estimate of the error rate: five or so errors a year out of “several hundred structures” is about 1% (not point in trying to estimate it any more accurately). That is comparable to the error rate which we find on Wikipedia when we check carefully – the latest audit figures I’ve seen indicate an error rate of less than 2% for WP, although it can sometimes be difficult to decide what we count as an “error”. C&EN is written by committed professionals, but they have to work to a journalistic timescale: Wikipedia is written by committable volunteers, but we have all the time in the world (it just doesn’t feel like it!)
Wikipedia certainly hopes to become a repository of well drawn structure images, although we cannot afford to pay professional artists as some publishers do! There are a number of problems which we are actively trying to address. Firstly, the structure has to be correct, as the domoic acid case shows! I would prefer a badly drawn structure which is correct than a well drawn structure which is wrong – I can always redraw the badly drawn structure but a false structure will just get perpetuated in the literature. Secondly, our users have to be able to find the structure – we have far more images than we actually use on our articles – and this requires some form of indexing. We’re working on these problems with a number of external partners – including ChemSpider, thanks a million guys for all your help! – and we hope to make some more formal announcements in the next few weeks.
May 21st, 2009 at 6:09 pm
Enjoyed reading this post. I personally do not pay much attention to details when it comes to chemical structures; paraphrasing well know quote “all chemical drawings are wrong, but some are useful”. I just wanted to let you know that apostrophes ( ’ or ‘ ) are not rendered correctly on my Firefox browser running on Linux (Fedora Core 10); I’m getting � , which seems to be a UTF and not ASCII. Thanks!