Hello Folks:
Kenyon College has access to a DSpace based archive system and is
awarding grants to utilize this resources. I would like to use this
to make a searchable archive of high quality NMR data from from
research compounds. Rolling review of grants begins tomorrow
(Saturday, May 15th, 2010) and the committee promises answers on
funding requests within 2-3 weeks. Following is a description of the
project. At the moment I am looking for an assessment of the
feasibility of the project and a quote. If funding is awarded, we
could move immediately into development. In addition to familiarity
with DSpace, working familiarity with either chemistry o
MarvinSketch and MarvinView would be ideal. Interested parties
should contact me at getzlery [at] kenyon (dot) edu or by phone at
740-427-5304.
Regards,
Yutan Getzler
Assistant Professor • Department of Chemistry
Kenyon College • Gambier, OH 43022-9623
In an idealized form, an NMR database would allow users, via a web
portal, to submit and retrieve the raw spectroscopic (~630 kb) and
supporting data. The supporting data would ideally include
information such as an image of the processed spectrum (~70 – 110 kb
as a .pdf), spectrum type (i.e. 1H, 13C, COSY, etc). synthetic
procedure, molecular structure, molecular formula, molecular weight,
IUPAC name, common name, etc. With the exception of the structure
data and the spectral image, the aforementioned are all text based
data. Ideally, a few simple automated checks could be built into the
system (e.g. do the molecular formula and molecular weight match the
structure, are all the expected portions of the files present?) which
would weed out egregious errors. Spectra would then go into a
holding state to be validated by registered experts, most likely
faculty, before being deposited in the database. Controlling the
level of accessibility would also be highly desirable – some data
could be kept on campus for use only in classes or research, while
other data could be made publicly available. In addition to being a
place where orphaned spectra could find a home, this could be a place
where higher quality versions of published data could be archived.
Construction of a structure based interface is perhaps the most
challenging aspect of this project, but it would make the database
most useful. Other long-term challenges are differences in data
formatting for different instruments. NMR spectroscopy is a well
developed field. Instruments have been commercially available for
nearly 50 years and this history, coupled with industry
consolidation, means there are three formats in which almost all
spectra are recorded. Kenyon uses a Bruker instrument, as do four of
the Five Colleges of Ohio, so an infrastructure for Bruker data would
support Kenyon and most of our peers. It would be ideal to build in
enough flexibility to accommodate expansion beyond Bruker. Finally,
I would like the option of mining the various forms of data submitted
and returning queries as a formatted pdf file.
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