Bringing spectroscopy into the COMCIFS fold

Peter Murray-Rust pm286 at cam.ac.uk
Wed Apr 5 08:43:11 BST 2017


On Tue, Apr 4, 2017 at 10:51 PM, Saulius Gra┼żulis <grazulis at ibt.lt> wrote:

> Hi, Peter,
>
> thanks for your comments!
>
> On 2017-02-23 11:25, Peter Murray-Rust wrote:
> > I have been interested in getting chemical spectroscopists to adopt
> > standards for publishing and sharing data for at least 20 years. In
> > short: there needs to be communal will and there isn't enough to drive a
> > useful process.
>
> Well, at the moment we need to set up smooth data exchange for our SOLSA
> project, so there is a need for common expandable spectroscopy standard;
> also, other people are looking for similar things, as I have learned
> recently.
>

Could be a good idea to post on the blueobelisk.org mailing list for ideas.


>
> The key point is that it needs to be simple -- we can not afford
> spending much time to implement a complicated format/standard.
>
> > There are standards - starting with JCAMP - which work
> > for many potential uses. JCAMP - 30 years old - can do much of what is
> > required for small to medium data sets and especially where there is a
> > single technique.dard is worth having, if only for that reason.
>
> ... Spectroscopy can be complicated (GC-MS-MS etc. So suggest we start
with 1-D spectra HNMR CNMR UV-VIS



> > Unless there is a clear organisation with a future driving the process I
> > think years could be spent getting nowhere.
>
> IUCr?
>

Worth asking. Let's suggest spectroscopy coupled to, or co-published with,
crystal structures. That could avoid  inter-Union sensitivities.

>
> > In short unless there is a strong spectroscopy champion I would not
> > develop in advance of market pull.
>
> We have several spectroscopy groups collaborating in our SOLSA project,
> and they expressed genuine interest in having a standard for data
> sharing. If we can come up with something simple enough, the investment
> is worth doing -- and then we'll see.
>

My suggestion is to create and deploy a working toolset. That exists.
People like Egon Willighagen and Chris Steinbeck will help. Show what can
be done.

>
> I would say a standard is only as good as the software that supports it,
> and only of there is considerable amount of available data in that
> standard. If we can get these then the effort is worth it.
>
> The worst thing that can happen is that people will start dumping
> spectra in CSV files from Excel, without any standard or ontology
> whatsoever. We would then risk loosing a lot of valuable measurements
> just because they are not properly documented.
>

The worst thing - and it happens several million times a year - is to dump
it as PDF, often bitmaps.
ARGHHH!


-- 
Peter Murray-Rust
Reader Emeritus in Molecular Informatics
Unilever Centre, Dept. Of Chemistry
University of Cambridge
CB2 1EW, UK
+44-1223-763069
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