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Re: Updating COMCIFS' approach to dictionaries

I approve of the general purpose here. Some details will need to be refined as we progress.

On Mon, Feb 20, 2012 at 1:16 AM, James Hester <jamesrhester@gmail.com> wrote:
>>Dear COMCIFS members,

I would appreciate hearing any thoughts on the issue discussed below.

I therefore envisage three levels of COMCIFS engagement with dictionaries:

(i) The Core CIF dictionary together with other small add-on
dictionaries continue to be treated as before, with active COMCIFS
approval required;

I agree. There is enough software and usage that the core dictionary must be managed carefully

>>(ii) Dictionaries that are submitted by organisations recognised
by COMCIFS as being competent are given automatic COMCIFS approval
(this would presumably apply, for example. to the PDB).  These
dictionaries are expected to maintain ontological agreement with other
IUCr dictionaries, and may require some technical editing;

I also agree with this. I have started to promote the dictionary approach in other areas  of physical science (computational chemistry, NMR spectroscopy). We ran a meeting here a month ago and BrianM presented the IUCr approach. It is seen as a shining light for others to follow.

We face the problem of "one true dictionary" against several local dictionaries without central direction. We are currently starting with one-dictionary-per-code (e.g. NWChem, Gaussian, etc.) - a bottom up approach - and also a single core dictionary with terms which are common to all experiments.

Currently we do not have organizations of the same initiative and coherence as IUCr/CIF so (iii) represents the starting point

>>(iii) COMCIFS offers syntactical checks and advice to dictionaries not
covered by (i) and (ii)

I think this will become common on the web outside crystallography. Like Herbert I would insist on namespaces. If there are two names for the same concept in different local dictionaries it's far better than having no local dictionaries. And the maintainers of those could agree that the names are synonyms and create a term in an uber-dictionary. We are going to have to deal with aliases, sameAs, etc. I don't think they should be encouraged, but it's primarily a social problem. The web has tools to address it

>>COMCIFS would also allow inclusion of any syntactically correct dictionaries in the central register maintained by the IUCr at the
disgression of the COMCIFS secretary, provided it is clear that
these dictionaries do not necessarily mesh with IUCr-sponsored dictionaries.

Fully agreed. It's how the world is developing.

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

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