I am an NMR spectroscopist by training. After a ten year stint at ACD/Labs managing their NMR product line for the first 6-7 years of that I went on to join a publisher (Royal Society of Chemistry). With that in mind I'd like to comment on Alan's statements. TO start...I AGREE!
The issue with online spectral databases isn't really a technology issue any longer...it's a participation issue.
NMRShiftDB is already online and has >43000 spectra from the community. These are structures with assignments. There have been a number of conversations online about this and this Google Search will highlight some of the conversations: http://tinyurl.com/294mb4p
However, in terms of spectral data, in the form of spectral curves, there have been numerous efforts to host online collections. Examples are:
1)
http://www.spectraonline.com/
2) Red Hen Spectra (see discussion here: http://cooper.edu/albert-nerken-school-of-engineering/outreach/projects/)
I have been working on an online database of spectral data for over 3 years as outlined in this poster
http://www.slideshare.net/AntonyWilliams/chem-spider-building-an-online-database-of-open-spectra
The benefits of this are that the NMR data are fed into an online game to help teach NMR as discussed here:
http://www.slideshare.net/AntonyWilliams/the-spectral-game-teaching-nmr-spectroscopy-via-a-web-browser
I've also given a presentation here about an online database of NMR spectra:
http://www.slideshare.net/AntonyWilliams/delivering-the-vision-of-an-online-database-of-nmr-spectra
ALan...publishers ARE already putting FIDs online. See this description here:
http://www.chemspider.com/blog/thieme-announce-access-to-doied-primary-analytical-data-available.html
When the data are made available this way then, as you say, they can be downloaded, processed and assembled onto online databases such as the one hosted at ChemSpider. Now I work for a publisher I can comment that I for one am interested in working further on this. The challenge is participation though...we cannot run spectra ourselves and even though we might be willing to host them and make them available as electronic files it is difficult to get people to submit them to us. Please note that depositors have data are NOT transferring copyright and that the data can be deposited as "Open Data". If anyone would like to discuss this that would be great!
Antony Williams PhD, FRSC
VP Strategic Development
ChemSpider, Royal Society of Chemistry
Phone: +1 (919) 201-1516
Fax: +1 (509)-275-6696
Email: williamsa_at_rsc.org<mailto:williamsa_at_rsc.org>
________________________________
From: Alan Kenwright [a.m.kenwright_at_durham.ac.uk]
Sent: Monday, November 15, 2010 4:44 AM
To: Yael Balazs
Cc: ammrl_at_ammrl.org
Subject: Re: AMMRL:kudos to Imperial College's SPECTRA
Hi All,
I could not get much useful information from the links (maybe they have been taken down), but I think Yael raises an important point. It is crazy in this age that we should still be relying on NMR data in the tabular form commonly reported in organic chemistry journals. However, I don't think that institution-run databases are the answer. Journals are the answer.
There are effectively only 3 data formats for NMR data from the major manufacturers plus a couple of other common formats. All are readable by common NMR processing software (MestreNova, ACDLabs and the like). The average 1D NMR data file is no larger than a fairly complicated figure in a paper. It should therefore be a requirement that when a new compound is reported in an org chem journal, the raw proton and carbon FID files are provided as part of the electronic supplementary information. Not a spectrum that has been carefully doctored up, but the raw data so that anyone else can download it and look at it as they see fit. It is amazing how much additional information is available there compared to the tabular report, not least of which is a ready assay of organic purity. More importantly, if you want to revisit the data, you are then working from the raw data, not somebody else's (less than impartial?) interpretation of it. And the advantages to people working on databases would be immense. I know that many journals now require a processed spectrum (as ESI) in addition to a tabular report in the text, but the ability to lodge the raw FID as well as (or even instead of) the processed spectrum would be a real step forward. (There is not even a significant overhead to producing the file - just zip or tar the data directory and send it).
The NMR community has really missed a trick here. There is no longer any technical reason for not doing this. We are quite lucky in that the limited number of available data formats (and their stability!) makes it entirely feasible. We just need to convince the journal editors. Unfortunately, the editors of Org Chem journals tend not to be NMR jocks.
If anyone has any ideas how to promote this I would be very grateful if they would share them.
Regards,
Alan.
Alan Kenwright
Reader in Spectroscopy
Chemistry Department
Durham University
On 14 Nov 2010, at 11:58, Yael Balazs wrote:
Hello spinlanders,
Quite likely that I'm behind the times and out of the loop - but I just noticed
Imperial College's SPECTRA D-space NMR repository:
https://spectradspace.lib.ic.ac.uk:8443/spectranmr/submission
via a "interactive table" link from a 2010 science article
(also cool: http://www.sciencemag.org/feature/data/1181771/)
For those who haven't seen it, also check out the explanatory page with
chemistry deposition tools (3. NMR Spectroscopy).
In my "NMR database - venting" post of February 2007, such a tool is exactly
what I had in mind.
A place where a journal reader could view the data from which the o-chem journal
style abbreviation was culled.
I'd like to extend my admiration and kudos to the developers of the SPECTRa
site. I'm looking forward to hearing about and seeing more such sites in the
future!
Best regards,
Yael
--
Yael S. Balazs, Ph.D. http://schulich.technion.ac.il/mrc
NMR Facility Manager phone: +972-4-829-3748
Schulich Faculty of Chemistry fax: +972-4-829-5703
Technion - Israel Institute of Technology
Haifa, Israel 32000 email: balazs_at_technion.ac.il
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Received on Mon Nov 15 2010 - 09:20:46 MST