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Re: Bringing spectroscopy into the COMCIFS fold

On Tue, Apr 4, 2017 at 10:51 PM, Saulius Gražulis <grazulis@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

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.


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.

Peter Murray-Rust
Reader Emeritus in Molecular Informatics
Unilever Centre, Dept. Of Chemistry
University of Cambridge

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